RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14045
(287 letters)
>gnl|CDD|215491 PLN02906, PLN02906, xanthine dehydrogenase.
Length = 1319
Score = 331 bits (851), Expect = e-105
Identities = 123/231 (53%), Positives = 159/231 (68%), Gaps = 8/231 (3%)
Query: 34 DACSKLNERLKPYKEKNPTGKWQDWVKAAFFDRTSLAATGYFKTPDIGYDMKKNEGAIFN 93
DAC ++ R++P K + + V A +F R L+A G++ TPDIG+D K +G FN
Sbjct: 1088 DACEQIKARMEPVASKLNFSSFAELVTACYFQRIDLSAHGFYITPDIGFDWKTGKGNPFN 1147
Query: 94 YFGYGASVSEVEIDCLTGDHQVRATEIVMDVGESLNPAIDVGQVEGAFMQGYGLYVMEEL 153
YF YGA+ +EVEID LTGD R +IVMD+G S+NPAID+GQ+EGAF+QG G +EEL
Sbjct: 1148 YFTYGAAFAEVEIDTLTGDFHTRRVDIVMDLGYSINPAIDIGQIEGAFVQGLGWVALEEL 1207
Query: 154 MFS-------PSGVLYTRGPGTYKIPGFADIPAEFNVSLLKGAPNPRAVYSSKAVGEPPL 206
+ G L+T GPGTYKIP DIP +FNVSLLKGAPNP+A++SSKAVGEPP
Sbjct: 1208 KWGDAAHKWIRPGSLFTCGPGTYKIPSVNDIPFKFNVSLLKGAPNPKAIHSSKAVGEPPF 1267
Query: 207 LLASSVYFAIRDAIDAYRKQELGREDYYRLDSPATPAKIRLLCEDSITKEF 257
LA+SV+FAI+DAI A R + G ++ LD+PATP +IR+ C D IT F
Sbjct: 1268 FLAASVFFAIKDAIKAARAEV-GLHGWFPLDTPATPERIRMACGDEITAPF 1317
>gnl|CDD|132014 TIGR02969, mam_aldehyde_ox, aldehyde oxidase. Members of this family
are mammalian aldehyde oxidase (EC 1.2.3.1) isozymes,
closely related to xanthine dehydrogenase/oxidase.
Length = 1330
Score = 293 bits (752), Expect = 4e-91
Identities = 129/240 (53%), Positives = 164/240 (68%), Gaps = 1/240 (0%)
Query: 33 QDACSKLNERLKPYKEKNPTGKWQDWVKAAFFDRTSLAATGYFKTPDIGYDMKKNEGAIF 92
+DAC L +RL+P KNP G W+DW + AF SL+A GYF+ + + +K EG F
Sbjct: 1092 KDACQTLLKRLEPIISKNPQGTWKDWAQTAFDQSISLSAVGYFRGYESNINWEKGEGHPF 1151
Query: 93 NYFGYGASVSEVEIDCLTGDHQVRATEIVMDVGESLNPAIDVGQVEGAFMQGYGLYVMEE 152
YF YGA+ SEVEIDCLTGDH+ T+IVMDVG S+NPA+D+GQVEGAF+QG GLY +EE
Sbjct: 1152 EYFVYGAACSEVEIDCLTGDHKNIRTDIVMDVGHSINPALDIGQVEGAFIQGMGLYTIEE 1211
Query: 153 LMFSPSGVLYTRGPGTYKIPGFADIPAEFNVSLLKGAPNPRAVYSSKAVGEPPLLLASSV 212
L +SP G+LY+RGP YKIP DIP E ++S L + + +YSSK +GE + L SV
Sbjct: 1212 LSYSPQGILYSRGPNQYKIPAICDIPTELHISFLPPSEHSNTLYSSKGLGESGVFLGCSV 1271
Query: 213 YFAIRDAIDAYRKQELGREDYYRLDSPATPAKIRLLCEDSITKEFPAPEPGSYKPWNISI 272
+FAI DA+ A R QE G ++L SP TP KIR+ CED TK P EPGSY PWN+ +
Sbjct: 1272 FFAIHDAVRAAR-QERGLSGPWKLTSPLTPEKIRMACEDKFTKMIPRDEPGSYVPWNVPV 1330
>gnl|CDD|226978 COG4631, XdhB, Xanthine dehydrogenase, molybdopterin-binding
subunit B [Nucleotide transport and metabolism].
Length = 781
Score = 228 bits (583), Expect = 2e-69
Identities = 100/246 (40%), Positives = 132/246 (53%), Gaps = 38/246 (15%)
Query: 33 QDACSKLNERLKPYKEKNPTGKWQ-----------------------DWVKAAFFDRTSL 69
QDA ++ ERL + W D VK A+F R L
Sbjct: 539 QDAARQIKERLVAFA----AEHWGVPEEDVAFLPNRVRIGGQELAFADLVKQAYFARVQL 594
Query: 70 AATGYFKTPDIGYDMKKNEGAIFNYFGYGASVSEVEIDCLTGDHQVRATEIVMDVGESLN 129
+A G++KTP I +D G F YF YGA+ SEV +D LTG+++V T+I+ DVG SLN
Sbjct: 595 SAAGFYKTPKIHWDRAAGRGRPFYYFAYGAACSEVSVDTLTGEYKVERTDILHDVGRSLN 654
Query: 130 PAIDVGQVEGAFMQGYGLYVMEELMFSPSGVLYTRGPGTYKIPGFADIPAEFNVSLLKGA 189
PAID+GQ+EG F+QG G EEL + G L T P TYKIP +D P FNV L + +
Sbjct: 655 PAIDLGQIEGGFVQGMGWLTTEELWWDEKGRLRTHAPSTYKIPLASDRPKIFNVRLAEWS 714
Query: 190 PNPRA-VYSSKAVGEPPLLLASSVYFAIRDAIDA---YRKQELGREDYYRLDSPATPAKI 245
N ++ SKAVGEPPL+L SV A+ DA+ + YR RLD+PATP ++
Sbjct: 715 ENAEPTIHRSKAVGEPPLMLGISVLEALSDAVASVADYRVCP-------RLDAPATPERV 767
Query: 246 RLLCED 251
+ E
Sbjct: 768 LMAVER 773
>gnl|CDD|200222 TIGR02965, xanthine_xdhB, xanthine dehydrogenase, molybdopterin
binding subunit. Members of the protein family are the
molybdopterin-containing large subunit (or, in,
eukaryotes, the molybdopterin-binding domain) of
xanthine dehydrogenase, and enzyme that reduces the
purine pool by catabolizing xanthine to urate. This
model is based primarily on bacterial sequences; it does
not manage to include all eukaryotic xanthine
dehydrogenases and thereby discriminate them from the
closely related enzyme aldehyde dehydrogenase [Purines,
pyrimidines, nucleosides, and nucleotides, Other].
Length = 758
Score = 225 bits (576), Expect = 2e-68
Identities = 93/200 (46%), Positives = 125/200 (62%), Gaps = 11/200 (5%)
Query: 56 QDWVKAAFFDRTSLAATGYFKTPDIGYDMKKNEGAIFNYFGYGASVSEVEIDCLTGDHQV 115
+ V+ A+F R L++TG++KTP I +D K G F YF YGA+ SEV +D LTG+++V
Sbjct: 564 AELVQQAYFARVQLSSTGFYKTPKIHWDRAKGRGRPFYYFAYGAACSEVSVDTLTGEYKV 623
Query: 116 RATEIVMDVGESLNPAIDVGQVEGAFMQGYGLYVMEELMFSPSGVLYTRGPGTYKIPGFA 175
+I+ DVG SLNPAID+GQ+EG F+QG G EEL++ G L T P TYKIP +
Sbjct: 624 LRADILHDVGRSLNPAIDIGQIEGGFVQGMGWLTTEELVWDEKGRLRTHAPSTYKIPAAS 683
Query: 176 DIPAEFNVSLLKGAPNPRA-VYSSKAVGEPPLLLASSVYFAIRDAIDA---YRKQELGRE 231
D P +FNV L + N ++ SKAVGEPPL+L SV FAI DA+ + YR
Sbjct: 684 DRPKDFNVRLFEWGENREDTIHRSKAVGEPPLMLGISVLFAISDAVASVADYRVCP---- 739
Query: 232 DYYRLDSPATPAKIRLLCED 251
RLD+PATP ++ + E
Sbjct: 740 ---RLDAPATPERVLMAVEA 756
>gnl|CDD|217210 pfam02738, Ald_Xan_dh_C2, Molybdopterin-binding domain of aldehyde
dehydrogenase.
Length = 543
Score = 197 bits (503), Expect = 2e-59
Identities = 76/154 (49%), Positives = 94/154 (61%), Gaps = 6/154 (3%)
Query: 31 CSQDACSKLNERLKPYKEKNP-----TGKWQDWVKAAFFDRTSLAATGYFKTPDIGYDMK 85
+ AC KL ERLKP K W+D + AA+ SL+AT + TP G++
Sbjct: 390 AVRLACEKLKERLKPIAAKMLEQSEEDITWEDGIVAAYGVSVSLSATAAYATPPTGFEPG 449
Query: 86 KN-EGAIFNYFGYGASVSEVEIDCLTGDHQVRATEIVMDVGESLNPAIDVGQVEGAFMQG 144
G F YF YGA+ EVE+DCLTGD +V T+IVMD G SLNPAID GQ+EG F+QG
Sbjct: 450 TGSYGTPFFYFTYGAAAVEVEVDCLTGDVKVLRTDIVMDCGTSLNPAIDEGQIEGGFVQG 509
Query: 145 YGLYVMEELMFSPSGVLYTRGPGTYKIPGFADIP 178
GL +MEE+++ P G L TR G YKIP DIP
Sbjct: 510 IGLALMEEIVYDPGGNLLTRSLGDYKIPTIDDIP 543
>gnl|CDD|215096 PLN00192, PLN00192, aldehyde oxidase.
Length = 1344
Score = 183 bits (466), Expect = 3e-52
Identities = 94/225 (41%), Positives = 132/225 (58%), Gaps = 20/225 (8%)
Query: 35 ACSKLNERLKPYKE----KNPTGKWQDWVKAAFFDRTSLAATGYFKTPDIGYDMKKNEGA 90
C L ERLKP KE + + W + A+ +L+A+ Y+ TPD +
Sbjct: 1115 CCVILVERLKPIKERLQEQMGSVTWDMLISQAYMQSVNLSASSYY-TPDP---------S 1164
Query: 91 IFNYFGYGASVSEVEIDCLTGDHQVRATEIVMDVGESLNPAIDVGQVEGAFMQGYGLYVM 150
Y YGA+VSEVE+D LTG+ + ++I+ D G+SLNPA+D+GQ+EGAF+QG G +++
Sbjct: 1165 SMEYLNYGAAVSEVEVDLLTGETTILRSDIIYDCGQSLNPAVDLGQIEGAFVQGIGFFML 1224
Query: 151 EELMFSPSGVLYTRGPGTYKIPGFADIPAEFNVSLLKGAPNPRAVYSSKAVGEPPLLLAS 210
EE + G++ T G TYKIP IP +FNV +L + + V SSKA GEPPLLLA+
Sbjct: 1225 EEYTTNSDGLVVTDGTWTYKIPTVDTIPKQFNVEILNSGHHKKRVLSSKASGEPPLLLAA 1284
Query: 211 SVYFAIRDAIDAYRKQEL------GREDYYRLDSPATPAKIRLLC 249
SV+ A R AI RKQ L G + ++L PAT ++ LC
Sbjct: 1285 SVHCATRAAIREARKQLLSWGGIDGSDSTFQLPVPATMPVVKELC 1329
>gnl|CDD|132240 TIGR03196, pucD, xanthine dehydrogenase D subunit. This gene has
been characterized in B. subtilis as the molybdopterin
binding-subunit of xanthine dehydrogenase (pucD), acting
in conjunction with pucC, the FAD-binding subunit and
pucE, the FeS-binding subunit. The more common XDH
complex (GenProp0640) includes the xdhB gene which is
related to pucD. It appears that most of the relatives
of pucD outside of this narrow clade are involved in
other processes as they are found in unrelated genomic
contexts, contain the more common XDH complex and/or do
not appear to process purines to allantoin.
Length = 768
Score = 75.8 bits (186), Expect = 2e-15
Identities = 42/140 (30%), Positives = 62/140 (44%), Gaps = 5/140 (3%)
Query: 95 FGYGASVSEVEIDCLTGDHQVRATEIVMDVGESLNPAIDVGQVEGAFMQGYGLYVMEELM 154
F A+ +EV++D GD ++ + G LNP GQ+EG GL +MEE
Sbjct: 630 FAAAAAAAEVDVDLDLGDVKLIDCAHAIAAGPVLNPLALRGQIEGGAAMALGLALMEEAK 689
Query: 155 FSPSGVLYTRGPGTYKIPGFADIPAEFNVSLLKGAPNPRAVYSSKAVGEPPLLLAS-SVY 213
+ G + Y IPG AD+P +++ A Y K VGE A+ ++
Sbjct: 690 MT-DGRVAAENFDDYLIPGIADVPDLDFIAIED--LMKDAPYGPKGVGEAGTCAATPAII 746
Query: 214 FAIRDAIDAY-RKQELGRED 232
AI DA+ K + ED
Sbjct: 747 AAIHDAVGCDINKLPIRPED 766
>gnl|CDD|224446 COG1529, CoxL, Aerobic-type carbon monoxide dehydrogenase, large
subunit CoxL/CutL homologs [Energy production and
conversion].
Length = 731
Score = 75.8 bits (187), Expect = 2e-15
Identities = 56/194 (28%), Positives = 83/194 (42%), Gaps = 23/194 (11%)
Query: 54 KWQDWVKAAFFDRTSLAATGYFKTPDIGYDMKKNEGAIFNYFGYGASVSEVEIDCLTGDH 113
D A +A G + + N + YGA ++EVE+D TG+
Sbjct: 553 GGGDRRSAV--SLKEVAGKGLAPGLAVAASFGSD-----NTYPYGAHIAEVEVDPETGEV 605
Query: 114 QVRATEIVMDVGESLNPAIDVGQVEGAFMQGYGLYVMEELMFSPSGVLYTRGPGTYKIPG 173
+V V D G +NP + GQVEG + G G+ + EE ++ G L Y IP
Sbjct: 606 RVLRVVAVDDCGRVVNPKLAEGQVEGGILMGIGMALYEEAIYDEDGQLLNSNLADYGIPR 665
Query: 174 FADIPAEFNVSLLKGAPNPRAVYSSKAVGEPPLLLASSVYFAIRDAI-DAYRKQELGRED 232
AD P E V ++ P+P +K VGE ++ + AI +A+ DA K
Sbjct: 666 AADAP-EVEVEFVES-PSPFGPLGAKGVGEGGII---GIAPAIANAVFDATGK------- 713
Query: 233 YYRLDS-PATPAKI 245
R+ P TP +I
Sbjct: 714 --RIRDLPITPERI 725
>gnl|CDD|182084 PRK09800, PRK09800, putative hypoxanthine oxidase; Provisional.
Length = 956
Score = 71.0 bits (174), Expect = 1e-13
Identities = 49/181 (27%), Positives = 84/181 (46%), Gaps = 30/181 (16%)
Query: 68 SLAATGYFKTPDIGYDMKKNEGAIFNYFGYGASVSEVEIDCLTGDHQVRATEIVMDVGES 127
SL TG + TPD F YGA+ +EV ++ TG+ ++ ++D G
Sbjct: 796 SLVGTGSYITPDFA-------------FPYGANFAEVAVNTRTGEIRLDKFYALLDCGTP 842
Query: 128 LNPAIDVGQVEGAFMQGYGLYVMEELMFSPSGVLYTRGPGTYKIPGFADIPAEFNVSLLK 187
+NP + +GQ+ GA ++ G + EE+++ G TR +Y P DIP +F L+
Sbjct: 843 VNPELALGQIYGATLRAIGHSMSEEIIYDAEGHPLTRDLRSYGAPKIGDIPRDFRAVLV- 901
Query: 188 GAPNPRAV--YSSKAVGEPPLLLAS-SVYFAIRDAIDAYRKQELGREDYYRLDSPATPAK 244
P+ V + +K++ E + A+ ++ AI DA + + + TP K
Sbjct: 902 --PSDDKVGPFGAKSISEIGVNGAAPAIATAIHDACGIWLR-----------EWHFTPEK 948
Query: 245 I 245
I
Sbjct: 949 I 949
>gnl|CDD|236637 PRK09970, PRK09970, xanthine dehydrogenase subunit XdhA;
Provisional.
Length = 759
Score = 69.3 bits (170), Expect = 3e-13
Identities = 40/131 (30%), Positives = 65/131 (49%), Gaps = 10/131 (7%)
Query: 93 NYFGYGASVSEVEIDCLTGDHQVRATEI--VMDVGESLNPAIDVGQVEGAFMQGYGLYVM 150
N +G + +VE+D +V I V D G LNP + GQV G G G +
Sbjct: 608 NPPAFGCTFVDVEVDIALC--KVTINRILNVHDSGHILNPLLAEGQVHGGMGMGIGWALF 665
Query: 151 EELMFSP-SGVLYTRGPGTYKIPGFADIPAEFNVSLLKGAPNPRAVYSSKAVGEPPLLLA 209
EE++ +GV+ YK+P D+P + + ++ P++ Y K++GEPP++
Sbjct: 666 EEMIIDEKTGVVRNPNLLDYKLPTMMDLP-QLESAFVE-IYEPQSAYGHKSLGEPPII-- 721
Query: 210 SSVYFAIRDAI 220
S AIR+A+
Sbjct: 722 -SPAPAIRNAV 731
>gnl|CDD|132356 TIGR03313, Se_sel_red_Mo, probable selenate reductase,
molybdenum-binding subunit. Our comparative genomics
suggests this protein family to be a subunit of a
selenium-dependent molybdenum hydroxylase, although the
substrate is not specified. This protein is suggested by
Bebien, et al., to be the molybdenum-binding subunit of
a molydbopterin-containing selenate reductase. Xi, et
al, however, show that mutation of this gene in E. coli
conferred sensitivity to adenine, suggesting a defect in
purine interconversion. This finding, plus homology of
nearby genes in a 23-gene purine catabolism region in E.
coli to xanthine dehydrogase subunits suggests xanthine
dehydrogenase activity.
Length = 951
Score = 68.5 bits (167), Expect = 7e-13
Identities = 37/136 (27%), Positives = 67/136 (49%), Gaps = 14/136 (10%)
Query: 68 SLAATGYFKTPDIGYDMKKNEGAIFNYFGYGASVSEVEIDCLTGDHQVRATEIVMDVGES 127
L TG + T + F YGA+ +EV ++ TG+ ++ ++D G
Sbjct: 792 QLVGTGSYITSEFA-------------FPYGANFAEVAVNTRTGEIRLDKFYALLDCGTP 838
Query: 128 LNPAIDVGQVEGAFMQGYGLYVMEELMFSPSGVLYTRGPGTYKIPGFADIPAEFNVSLLK 187
+NP + +GQ+ GA M+ G + EE+++ +G+ TR +Y P DIP +F L+
Sbjct: 839 VNPELALGQIYGATMRAIGHSMTEEIVYDDNGIPLTRDLKSYGAPKIGDIPRDFRAVLVP 898
Query: 188 GAPNPRAVYSSKAVGE 203
+ + Y +K++ E
Sbjct: 899 -SDDKVGPYGAKSISE 913
>gnl|CDD|132238 TIGR03194, 4hydrxCoA_A, 4-hydroxybenzoyl-CoA reductase, alpha
subunit. This model represents the largest chain,
alpha, of the enzyme 4-hydroxybenzoyl-CoA reductase. In
species capable of degrading various aromatic compounds
by way of benzoyl-CoA, this enzyme can convert
4-hydroxybenzoyl-CoA to benzoyl-CoA.
Length = 746
Score = 62.1 bits (151), Expect = 8e-11
Identities = 52/199 (26%), Positives = 88/199 (44%), Gaps = 19/199 (9%)
Query: 51 PTGKWQDWVKAAFFDRTSLAATGYFKTPDIGYDMKKNEGAIFNY--FGYGASVSEVEIDC 108
P +Q+ VKAA D ++ G + P KK GA+ + F Y A V EV +D
Sbjct: 559 PGLSFQEVVKAALVDSGTITVKGTYTCPPEFQGGKKRGGAVGSTMGFSYAAQVVEVSVDE 618
Query: 109 LTGDHQVRATEIVMDVGESLNPAIDVGQVEGAFMQGYGLYVMEELMFSPSGVLYTRGPGT 168
TG V + +D G+++NP GQV+GA G G + EE ++ +G +
Sbjct: 619 ETGKVTVHKVWVAVDCGKAINPLAVEGQVQGAVWMGMGQALSEETVYD-NGRMKHASLLD 677
Query: 169 YKIPGFADIPAEFNVSLLKGAPNPRAVYSSKAVGEPPLL-LASSVYFAIRDAIDAYRKQE 227
Y++P + P + V +++ +P + +K E L +++ A+ DA+
Sbjct: 678 YRVPTIVESP-DIEVIIVESM-DPNGPFGAKEASEGALAGFLPAIHNAVYDAVGV----- 730
Query: 228 LGREDYYRLDS-PATPAKI 245
R P TP ++
Sbjct: 731 -------RATDLPLTPDRV 742
>gnl|CDD|131469 TIGR02416, CO_dehy_Mo_lg, carbon-monoxide dehydrogenase, large
subunit. This model represents the large subunits of
group of carbon-monoxide dehydrogenases that include
molybdenum as part of the enzymatic cofactor. There are
various forms of carbon-monoxide dehydrogenase;
Salicibacter pomeroyi DSS-3, for example, has two forms.
Note that, at least in some species, the active site Cys
is modified with a selenium attached to (rather than
replacing) the sulfur atom. This is termed
selanylcysteine, and created post-translationally, in
contrast to selenocysteine incorporation during
translation as for many other selenoproteins [Energy
metabolism, Other].
Length = 770
Score = 50.7 bits (121), Expect = 5e-07
Identities = 32/114 (28%), Positives = 52/114 (45%), Gaps = 8/114 (7%)
Query: 95 FGYGASVSEVEIDCLTGDHQVRATEIVMDVGESLNPAIDVGQVEGAFMQGYGLYVMEELM 154
+ +GA V+ID TG +VR + D G +NP I GQ+ G +G+ + + +E+
Sbjct: 626 YPFGAYFCVVDIDVDTGVAKVRRFYALDDCGTRINPMIIEGQIHGGLTEGFAVAMGQEIR 685
Query: 155 FSPSGVLYTRGPGTYKIPGFADIP---AEFNVSLLKGAPNPRAVYSSKAVGEPP 205
F G + Y +P + P + V+ P+P +K VGE P
Sbjct: 686 FDEQGNVLGASLMDYFLPTAVETPHWETDHTVT-----PSPHHPIGAKGVGESP 734
>gnl|CDD|132354 TIGR03311, Se_dep_Molyb_1, selenium-dependent molybdenum
hydroxylase 1. Members of this protein family show full
length homology to the molybdenum-containing aldehyde
oxido-reductase of Desulfovibrio gigas. Members,
however, are found only within species that have, and
near those genes that encode, a set of predicted
accessory proteins for selenium-dependent molybdenum
hydroxylases. The best known examples of such enzymes
are forms of xanthine dehydrogenase and purine
hydroxylase; this family appears to be another such
enzyme.
Length = 848
Score = 33.3 bits (76), Expect = 0.16
Identities = 25/81 (30%), Positives = 36/81 (44%), Gaps = 4/81 (4%)
Query: 123 DVGESLNPAIDVGQVEGAFMQGYGLYVMEELMFSPSGVLYTRGPGTYKIPGFADIPAEFN 182
DVG ++NP GQ+EG + G G + E+ T GT + +P E
Sbjct: 738 DVGRAINPLNLEGQIEGGIVMGLGYALTEDFPLREGIP--TAKFGTLGLFRSTQVP-EIE 794
Query: 183 VSLLKGAPNPRAVYSSKAVGE 203
L++ P A Y +K VGE
Sbjct: 795 THLIEKNGTPLA-YGAKGVGE 814
>gnl|CDD|129582 TIGR00491, aIF-2, translation initiation factor aIF-2/yIF-2. This
model describes archaeal and eukaryotic orthologs of
bacterial IF-2. Like IF-2, it helps convey the initiator
tRNA to the ribosome, although the initiator is
N-formyl-Met in bacteria and Met here. This protein is
not closely related to the subunits of eIF-2 of
eukaryotes, which is also involved in the initiation of
translation. The aIF-2 of Methanococcus jannaschii
contains a large intein interrupting a region of very
strongly conserved sequence very near the amino end; the
alignment generated by This model does not correctly
align the sequences from Methanococcus jannaschii and
Pyrococcus horikoshii in this region [Protein synthesis,
Translation factors].
Length = 590
Score = 30.6 bits (69), Expect = 1.1
Identities = 15/70 (21%), Positives = 30/70 (42%), Gaps = 7/70 (10%)
Query: 179 AEFNVSLLKGAPNPRAVYSSKAVGEPPLLLASSVYFAIRDAIDAYRKQELGREDYYRLDS 238
FNV +L GA Y K L + ++ + + + + + + + +++
Sbjct: 408 IAFNVKVLPGAEQELKKYDIK-------LFSDNIIYRLMEEFEEWIEGIEEEKKRKWMEA 460
Query: 239 PATPAKIRLL 248
PAKIRL+
Sbjct: 461 IIKPAKIRLI 470
>gnl|CDD|148658 pfam07182, DUF1402, Protein of unknown function (DUF1402). This
family consists of several hypothetical bacterial
proteins of around 310 residues in length. Members of
this family seem to be found exclusively in
Agrobacterium, Rhizobium and Brucella species. The
function of this family is unknown.
Length = 304
Score = 29.7 bits (67), Expect = 1.7
Identities = 18/38 (47%), Positives = 25/38 (65%), Gaps = 7/38 (18%)
Query: 189 APNPRAVYSSKAVGEPPLLLASSVYFA--IRDAIDAYR 224
A +P+AVY +A+ +P LA Y A IRD+IDAY+
Sbjct: 209 ADDPQAVY--RAIMDPDRSLA---YIAAIIRDSIDAYK 241
>gnl|CDD|132727 cd06929, NR_LBD_F1, Ligand-binding domain of nuclear receptor
family 1. Ligand-binding domain (LBD) of nuclear
receptor (NR) family 1: This is one of the major
subfamily of nuclear receptors, including thyroid
receptor, retinoid acid receptor, ecdysone receptor,
farnesoid X receptor, vitamin D receptor, and other
related receptors. Nuclear receptors form a superfamily
of ligand-activated transcription regulators, which
regulate various physiological functions, from
development, reproduction, to homeostasis and metabolism
in animals (metazoans). The family contains not only
receptors for known ligands but also orphan receptors
for which ligands do not exist or have not been
identified. NRs share a common structural organization
with a central well conserved DNA binding domain (DBD),
a variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD).
Length = 174
Score = 29.1 bits (66), Expect = 1.9
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 170 KIPGFADIPAEFNVSLLKGA 189
+IPGF ++ E ++LLKG
Sbjct: 24 RIPGFRELSQEDQIALLKGG 43
>gnl|CDD|216326 pfam01142, TruD, tRNA pseudouridine synthase D (TruD). TruD is
responsible for synthesis of pseudouridine from
uracil-13 in transfer RNAs. The structure of TruD
reveals an overall V-shaped molecule which contains an
RNA-binding cleft.
Length = 336
Score = 29.5 bits (67), Expect = 2.0
Identities = 9/31 (29%), Positives = 12/31 (38%)
Query: 233 YYRLDSPATPAKIRLLCEDSITKEFPAPEPG 263
Y P ++R ED I +E EP
Sbjct: 7 PYLTGKPGIGGRLRQTPEDFIVEEILGFEPS 37
>gnl|CDD|199877 cd06910, M14_ASTE_ASPA_like_7, Peptidase M14 Succinylglutamate
desuccinylase (ASTE)/aspartoacylase (ASPA)-like;
uncharacterized subgroup. A functionally
uncharacterized subgroup of the Succinylglutamate
desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily
which is part of the M14 family of
metallocarboxypeptidases. ASTE catalyzes the fifth and
last step in arginine catabolism by the arginine
succinyltransferase pathway, and aspartoacylase (ASPA,
also known as aminoacylase 2, and ACY-2; EC:3.5.1.15)
cleaves N-acetyl L-aspartic acid (NAA) into aspartate
and acetate. NAA is abundant in the brain, and
hydrolysis of NAA by ASPA may help maintain white
matter. ASPA is an NAA scavenger in other tissues.
Mutations in the gene encoding ASPA cause Canavan
disease (CD), a fatal progressive neurodegenerative
disorder involving dysmyelination and spongiform
degeneration of white matter in children. This enzyme
binds zinc which is necessary for activity. Measurement
of elevated NAA levels in urine is used in the diagnosis
of CD.
Length = 272
Score = 28.8 bits (65), Expect = 3.5
Identities = 11/39 (28%), Positives = 16/39 (41%), Gaps = 1/39 (2%)
Query: 108 CLTGDHQVRATEIVMDVGESLNPAIDVGQVEGAFMQGYG 146
L GD Q + + VG+ D G G ++ YG
Sbjct: 111 ILAGDLQ-KGRALARAVGDPATVVADAGHAAGRRLRDYG 148
>gnl|CDD|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in
azoospermia-like (DAZL) proteins. This subgroup
corresponds to the RRM of DAZL, also termed
SPGY-like-autosomal, encoded by the autosomal homolog of
DAZ gene, DAZL. It is ancestral to the deleted in
azoospermia (DAZ) protein. DAZL is germ-cell-specific
RNA-binding protein that contains a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and a DAZ motif, a
protein-protein interaction domain. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 82
Score = 27.1 bits (60), Expect = 3.7
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 81 GYDMKKNEGAIFNYFGYGASVSEVEI 106
G D++ +E I ++F SV EV+I
Sbjct: 12 GIDIRMDETEIRSFFAKYGSVKEVKI 37
>gnl|CDD|132743 cd06945, NR_LBD_Nurr1_like, The ligand binding domain of Nurr1 and
related nuclear receptor proteins, members of nuclear
receptor superfamily. The ligand binding domain of
nuclear receptor Nurr1_like: This family of nuclear
receptors, including Nurr1, Nerve growth
factor-induced-B (NGFI-B) and DHR38 are involved in the
embryo development. Nurr1 is a transcription factor that
is expressed in the embryonic ventral midbrain and is
critical for the development of dopamine (DA) neurons.
Structural studies have shown that the ligand binding
pocket of Nurr1 is filled by bulky hydrophobic residues,
making it unable to bind to ligands. Therefore, it
belongs to the class of orphan receptors. However, Nurr1
forms heterodimers with RXR and can promote signaling
via its partner, RXR. NGFI-B is an early immediate gene
product of embryo development that is rapidly produced
in response to a variety of cellular signals including
nerve growth factor. It is involved in T-cell-mediated
apoptosis, as well as neuronal differentiation and
function. NGFI-B regulates transcription by binding to a
specific DNA target upstream of its target genes and
regulating the rate of tr anscriptional initiation.
Another group of receptor in this family is DHR38.
DHR38 is the Drosophila homolog to the vertebrate
NGFI-B-type orphan receptor. It interacts with the USP
component of the ecdysone receptor complex, suggesting
that DHR38 might modulate ecdysone-triggered signals in
the fly, in addition to the ECR/USP pathway. Nurr1_like
proteins exhibit a modular structure that is
characteristic for nuclear receptors; they have a
central well conserved DNA binding domain (DBD), a
variable N-terminal domain, a non-conserved hinge and a
C-terminal ligand binding domain (LBD).
Length = 239
Score = 28.1 bits (63), Expect = 5.1
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 168 TYKIPGFADIPAEFNVSLLKGA 189
KIPGF D+ E LL+ A
Sbjct: 61 AEKIPGFKDLHREDQDLLLESA 82
>gnl|CDD|221066 pfam11300, DUF3102, Protein of unknown function (DUF3102). This
family of proteins has no known function.
Length = 130
Score = 27.4 bits (61), Expect = 5.5
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 42 RLKPYKEKNPTGKWQDWVKAAF 63
RLK K P G+W W+K +
Sbjct: 31 RLKEAKALLPHGEWGKWLKESV 52
>gnl|CDD|226637 COG4167, SapF, ABC-type antimicrobial peptide transport system,
ATPase component [Defense mechanisms].
Length = 267
Score = 27.9 bits (62), Expect = 5.7
Identities = 12/30 (40%), Positives = 17/30 (56%), Gaps = 3/30 (10%)
Query: 111 GDHQVRATEIVM---DVGESLNPAIDVGQV 137
GD+ R+ I M D SLNP + +GQ+
Sbjct: 80 GDYSFRSKRIRMIFQDPNTSLNPRLRIGQI 109
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
0.317 0.135 0.417
Gapped
Lambda K H
0.267 0.0687 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,043,239
Number of extensions: 1436026
Number of successful extensions: 1085
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1071
Number of HSP's successfully gapped: 26
Length of query: 287
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 191
Effective length of database: 6,679,618
Effective search space: 1275807038
Effective search space used: 1275807038
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 (21.6 bits)
S2: 58 (26.2 bits)