RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11686
(939 letters)
>gnl|CDD|239029 cd02111, eukary_SO_Moco, molybdopterin binding domain of sulfite
oxidase (SO). SO catalyzes the terminal reaction in the
oxidative degradation of the sulfur-containing amino
acids cysteine and methionine. Common features of all
known members of the sulfite oxidase (SO) family of
molybdopterin binding domains are that they contain one
single pterin cofactor and part of the coordination of
the metal (Mo) is a cysteine ligand of the protein and
that they catalyze the transfer of an oxygen to or from
a lone pair of electrons on the substrate.
Length = 365
Score = 180 bits (459), Expect = 6e-50
Identities = 75/130 (57%), Positives = 94/130 (72%), Gaps = 2/130 (1%)
Query: 248 GKVILSDHESTSHWQQNDYKGFSPSTDWDTVDFAKSPAIQELPVISAICLP-VADAKLKL 306
++++SD ES SHWQQNDYKGFSPS DWD VDF+K+PAIQE+PV SAIC P V + +
Sbjct: 200 DRIVVSDEESDSHWQQNDYKGFSPSVDWDNVDFSKAPAIQEMPVQSAICSPSVGAPVVTV 259
Query: 307 ENHQMEVQGYAWSGGGKAIVRVDVTIDQGRTWHVANFTGQDSQAPLTRHWGWTLWRATIP 366
++ V+GYAWSGGG+ IVRVDV++D GRTW VA +++ P R W WTLW AT+P
Sbjct: 260 PPGKITVKGYAWSGGGRKIVRVDVSLDGGRTWKVAELEQEENVWPSGRKWAWTLWEATVP 319
Query: 367 VDPKTKEVSI 376
V P KE I
Sbjct: 320 V-PAGKEAEI 328
Score = 72.0 bits (177), Expect = 3e-13
Identities = 29/52 (55%), Positives = 36/52 (69%), Gaps = 3/52 (5%)
Query: 470 SLDSADV---QHVHVEIWSKAVDSSYNTQPESFANIWNLRGVLSNAYHRVRV 518
+L A V EI +KAVDS+YN QPE+ IWNLRGVL+NA+HRV+V
Sbjct: 312 TLWEATVPVPAGKEAEIIAKAVDSAYNVQPETVEPIWNLRGVLNNAWHRVKV 363
Score = 67.0 bits (164), Expect = 1e-11
Identities = 28/50 (56%), Positives = 29/50 (58%), Gaps = 3/50 (6%)
Query: 433 VKPVKGLTWGHAAVGNATWTGARLVDVLKAAGISPDQSLDSADVQHVHVE 482
VK VKGL WG A+ NA W GARL DVL AGI D S HVH E
Sbjct: 91 VKKVKGLQWGDGAISNAEWGGARLRDVLLDAGIPEDDSQGGL---HVHFE 137
Score = 44.7 bits (106), Expect = 1e-04
Identities = 16/29 (55%), Positives = 21/29 (72%)
Query: 124 LKATSLKPYNAEPPPSMLVENFLTPSLLS 152
LK S KP+NAEPP S+L +F+TP+ L
Sbjct: 2 LKVNSKKPFNAEPPSSLLASSFITPNELF 30
Score = 42.0 bits (99), Expect = 0.001
Identities = 27/112 (24%), Positives = 37/112 (33%), Gaps = 24/112 (21%)
Query: 433 VKPVKGLTWGHAAVGNATWTG-----ARLVDVLKAAGISPDQ-SLDSADVQHVHVEIWSK 486
PV + G V W+G R VDV G + L+ + W+
Sbjct: 253 GAPVVTVPPGKITVKGYAWSGGGRKIVR-VDVSLDGGRTWKVAELEQEENVWPSGRKWAW 311
Query: 487 AVDSSYNTQPESFANIWNLRGVLSNAYHRVRVEIWSKAVDSSYNTQPENGHP 538
+ + P EI +KAVDS+YN QPE P
Sbjct: 312 TLWEATVPVPAGKE-----------------AEIIAKAVDSAYNVQPETVEP 346
Score = 34.3 bits (79), Expect = 0.31
Identities = 14/21 (66%), Positives = 16/21 (76%)
Query: 217 LKATSLKPYNAEPPPSMLYSS 237
LK S KP+NAEPP S+L SS
Sbjct: 2 LKVNSKKPFNAEPPSSLLASS 22
>gnl|CDD|217537 pfam03404, Mo-co_dimer, Mo-co oxidoreductase dimerisation domain.
This domain is found in molybdopterin cofactor (Mo-co)
oxidoreductases. It is involved in dimer formation, and
has an Ig-fold structure.
Length = 130
Score = 107 bits (270), Expect = 2e-27
Identities = 32/94 (34%), Positives = 52/94 (55%)
Query: 284 PAIQELPVISAICLPVADAKLKLENHQMEVQGYAWSGGGKAIVRVDVTIDQGRTWHVANF 343
AI +L V SAIC P ++KL ++GYA+SGGG+ I RV+V++D G++W +A+
Sbjct: 2 YAIYDLNVNSAICSPEHGERVKLGAGTYTIKGYAYSGGGRRITRVEVSLDGGKSWRLADI 61
Query: 344 TGQDSQAPLTRHWGWTLWRATIPVDPKTKEVSIM 377
++ + + + W W +PV IM
Sbjct: 62 DYEEDRYRYEKCFCWCFWSLDVPVSELLGAKEIM 95
Score = 57.7 bits (140), Expect = 6e-10
Identities = 19/40 (47%), Positives = 28/40 (70%), Gaps = 2/40 (5%)
Query: 482 EIWSKAVDSSYNTQPESFANIWNLRGVLSNAYHRVRVEIW 521
EI +AVD S N QPE WN+RG+++NA+HRV++ +
Sbjct: 93 EIMVRAVDESGNVQPEDM--YWNVRGMMNNAWHRVKIHVE 130
Score = 33.1 bits (76), Expect = 0.23
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 517 RVEIWSKAVDSSYNTQPEN 535
EI +AVD S N QPE+
Sbjct: 91 AKEIMVRAVDESGNVQPED 109
>gnl|CDD|223690 COG0617, PcnB, tRNA nucleotidyltransferase/poly(A) polymerase
[Translation, ribosomal structure and biogenesis].
Length = 412
Score = 94.4 bits (235), Expect = 2e-20
Identities = 42/162 (25%), Positives = 62/162 (38%), Gaps = 10/162 (6%)
Query: 649 DGTVYDYFNGHEDLKKGVCAFVGDPVSRIQEDYLRILRYFRFFARICNNPNNHKEEVLSA 708
DG + D F G +DL+ V +GD R +ED LRILR RF AR + E A
Sbjct: 126 DGEIIDPFGGLKDLENRVLRHIGDASERFREDPLRILRAARFAAR---LGFTIEPETEEA 182
Query: 709 IKNNLDGLHNISGERIWTELNKILGGSFSKEMMLKM----LYQNLLLFSKLKATTMREYI 764
I+ L IS ER+W EL K+L +E + + + +LF +L +
Sbjct: 183 IRLMAPLLAKISRERLWDELKKLLLSPNPREALQLLREYGALK--ILFPELDKLFGVPKL 240
Query: 765 VELMKYKEKSELIKDFH-KWRLPTFPMNGNIIRQFFARICNN 805
+ ++ E D P +
Sbjct: 241 LLALREIELLLHNTDELLLALAALLPAFLLAAATLPLLLRKG 282
Score = 50.9 bits (122), Expect = 2e-06
Identities = 23/56 (41%), Positives = 32/56 (57%), Gaps = 6/56 (10%)
Query: 378 DMLMGKKPHDIDFATNATPDQMKAMFAEEKVRTFNEKGEKHGTVCARMNDKENFEV 433
D+L+G+ P D+D ATNATP+++K +F R G K GTV + E EV
Sbjct: 34 DLLLGRPPKDVDIATNATPEEVKKLFR--NTR---PVGRKFGTVTV-PFNGEIIEV 83
Score = 50.1 bits (120), Expect = 4e-06
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 898 ITTLRIDV-TTDGRHAEVQFTEDWKLDANRRDLTVNSMF 935
+TT R + +GR V F + D RRD T+N++
Sbjct: 83 VTTFRKEGYGYNGRPLPVVFPGTLEEDLKRRDFTINALA 121
Score = 42.4 bits (100), Expect = 9e-04
Identities = 16/51 (31%), Positives = 22/51 (43%)
Query: 811 EEVLSAIKKNLDGLHNISGERIWTELNKILGGSFSKEMMLKMLEINMFPHL 861
E AI+ L IS ER+W EL K+L +E + + E L
Sbjct: 177 PETEEAIRLMAPLLAKISRERLWDELKKLLLSPNPREALQLLREYGALKIL 227
>gnl|CDD|239028 cd02110, SO_family_Moco_dimer, Subgroup of sulfite oxidase (SO)
family molybdopterin binding domains that contains
conserved dimerization domain. This molybdopterin
cofactor (Moco) binding domain is found in a variety of
oxidoreductases, main members of this family are nitrate
reductase (NR) and sulfite oxidase (SO). .
Length = 317
Score = 85.8 bits (213), Expect = 5e-18
Identities = 39/123 (31%), Positives = 54/123 (43%), Gaps = 9/123 (7%)
Query: 252 LSDHESTSHWQQNDYKGFSPSTDWDTVDFAKSPAIQELPVISAICLPVADAKLKLENHQM 311
++D S +WQ DY P D V I E+PV S I P + + ++
Sbjct: 169 VTDQPSDGYWQTRDYTVPPPDVDA--VGGKARRPIGEMPVKSVITSP-SPGAELVSGGRV 225
Query: 312 EVQGYAWSGGGKAIVRVDVTIDQGRTWHVANFTGQDSQAPLTRHWGWTLWRATIPVDPKT 371
E+ G AWSGG I RV+V++D GRTW A + PL W W + P
Sbjct: 226 EIGGVAWSGGRG-IRRVEVSLDGGRTWQEARL-----EGPLAGPRAWRQWELDWDLPPGE 279
Query: 372 KEV 374
E+
Sbjct: 280 YEL 282
Score = 55.0 bits (133), Expect = 6e-08
Identities = 29/93 (31%), Positives = 40/93 (43%), Gaps = 10/93 (10%)
Query: 435 PVKGLTW-GHAAV--------GNATWTGARLVDVLKAAGISPDQSLDSADVQHVHVEIWS 485
+ G+ W G + G TW ARL L LD D+ E+ +
Sbjct: 226 EIGGVAWSGGRGIRRVEVSLDGGRTWQEARLEGPLAGPRAWRQWELD-WDLPPGEYELVA 284
Query: 486 KAVDSSYNTQPESFANIWNLRGVLSNAYHRVRV 518
+A DS+ N QPE WN G +N +HRV+V
Sbjct: 285 RATDSTGNVQPERAEWNWNPGGYGNNHWHRVQV 317
Score = 51.9 bits (125), Expect = 7e-07
Identities = 18/35 (51%), Positives = 21/35 (60%)
Query: 434 KPVKGLTWGHAAVGNATWTGARLVDVLKAAGISPD 468
G WGH AVGNA WTG L D+L+ AG+ P
Sbjct: 61 PVRSGAQWGHGAVGNARWTGVPLKDLLEEAGVKPG 95
Score = 34.6 bits (80), Expect = 0.19
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 8/43 (18%)
Query: 503 WNLRGVLSNAYHRVRVEIWSKAVDSSYNTQPE----NGHPSGY 541
W L L + E+ ++A DS+ N QPE N +P GY
Sbjct: 269 WELDWDLPPGEY----ELVARATDSTGNVQPERAEWNWNPGGY 307
>gnl|CDD|177772 PLN00177, PLN00177, sulfite oxidase; Provisional.
Length = 393
Score = 83.0 bits (205), Expect = 9e-17
Identities = 43/125 (34%), Positives = 67/125 (53%), Gaps = 7/125 (5%)
Query: 256 ESTSHWQQNDYKGFSPSTDWDTVDFAKSPAIQELPVISAICLPVADAKLKLENHQMEVQG 315
E + Q DYK F PS +WD ++++ + PV SAIC + D ++ ++ V G
Sbjct: 231 ECQGFFMQKDYKMFPPSVNWDNINWSTRRPQMDFPVQSAIC-SLEDVNA-IKPGKVTVAG 288
Query: 316 YAWSGGGKAIVRVDVTIDQGRTWHVANFTGQD-----SQAPLTRHWGWTLWRATIPVDPK 370
YA SGGG+ I RVD+++D G+TW A+ + S + W W L+ AT+ V
Sbjct: 289 YALSGGGRGIERVDISVDGGKTWVEASRYQKPGVPYISDDISSDKWAWVLFEATVDVPQS 348
Query: 371 TKEVS 375
T+ V+
Sbjct: 349 TEIVA 353
Score = 61.8 bits (150), Expect = 8e-10
Identities = 33/81 (40%), Positives = 43/81 (53%), Gaps = 10/81 (12%)
Query: 447 GNATWTGARLVDVLKAAGISPDQSLD---------SADVQHVHVEIWSKAVDSSYNTQPE 497
G TW A IS D S D + DV EI +KAVDS+ N QPE
Sbjct: 307 GGKTWVEASRYQKPGVPYISDDISSDKWAWVLFEATVDVPQ-STEIVAKAVDSAANVQPE 365
Query: 498 SFANIWNLRGVLSNAYHRVRV 518
S +IWNLRG+L+ ++HRV++
Sbjct: 366 SVESIWNLRGILNTSWHRVQL 386
Score = 49.9 bits (119), Expect = 5e-06
Identities = 23/58 (39%), Positives = 34/58 (58%)
Query: 422 CARMNDKENFEVKPVKGLTWGHAAVGNATWTGARLVDVLKAAGISPDQSLDSADVQHV 479
CA +V+ V+G+ W +A+GNA W GA+L DVL+ GI S+ S+ +HV
Sbjct: 98 CAGNRRTAMSKVRKVRGVGWDVSAIGNAVWGGAKLADVLELVGIPKLTSITSSGGKHV 155
Score = 44.8 bits (106), Expect = 2e-04
Identities = 18/35 (51%), Positives = 24/35 (68%)
Query: 114 YVMEPVRSPLLKATSLKPYNAEPPPSMLVENFLTP 148
Y EP R P LK + +P+NAEPP S LV +++TP
Sbjct: 10 YSQEPPRHPSLKINAKEPFNAEPPRSALVSSYITP 44
Score = 39.5 bits (92), Expect = 0.008
Identities = 17/31 (54%), Positives = 20/31 (64%)
Query: 207 YVMEPVRSPLLKATSLKPYNAEPPPSMLYSS 237
Y EP R P LK + +P+NAEPP S L SS
Sbjct: 10 YSQEPPRHPSLKINAKEPFNAEPPRSALVSS 40
Score = 29.8 bits (67), Expect = 6.8
Identities = 11/17 (64%), Positives = 14/17 (82%)
Query: 519 EIWSKAVDSSYNTQPEN 535
EI +KAVDS+ N QPE+
Sbjct: 350 EIVAKAVDSAANVQPES 366
>gnl|CDD|239030 cd02112, eukary_NR_Moco, molybdopterin binding domain of eukaryotic
nitrate reductase (NR). Assimilatory NRs catalyze the
reduction of nitrate to nitrite which is subsequently
converted to NH4+ by nitrite reductase. Eukaryotic
assimilatory nitrate reductases are cytosolic
homodimeric enzymes with three prosthetic groups, flavin
adenine dinucleotide (FAD), cytochrome b557, and Mo
cofactor, which are located in three functional domains.
Common features of all known members of the sulfite
oxidase (SO) family of molybdopterin binding domains are
that they contain one single pterin cofactor and part of
the coordination of the metal (Mo) is a cysteine ligand
of the protein and that they catalyze the transfer of an
oxygen to or from a lone pair of electrons on the
substrate.
Length = 386
Score = 77.8 bits (192), Expect = 5e-15
Identities = 39/153 (25%), Positives = 72/153 (47%), Gaps = 13/153 (8%)
Query: 249 KVILSDHESTSHWQQNDYKGFSPSTDWDTVD----FAKSP-AIQELPVISAICLP----V 299
++++SD ES +H+ +D + D + + + K I +L V SAI P V
Sbjct: 217 RIVVSDRESQNHYHFHDNRVLPSHVDAELANEEGWWYKPEYIINDLNVNSAITTPAHDEV 276
Query: 300 ADAKLKLENHQMEVQGYAWSGGGKAIVRVDVTIDQGRTWHVANFTGQDSQAPLTRHWGWT 359
++GYA++GGG+ + RV+V++D G++W +A+ + + W W
Sbjct: 277 LPLNGLTTAETYTMKGYAYAGGGRRVTRVEVSLDDGKSWKLASIDYPEDPTKYGKCWCWC 336
Query: 360 LWRATIPVDP--KTKEVSI--MDMLMGKKPHDI 388
W +P+ KE+ + D M +P D+
Sbjct: 337 FWSLDVPLSELLAAKEICVRAWDESMNTQPRDM 369
Score = 50.5 bits (121), Expect = 3e-06
Identities = 19/48 (39%), Positives = 21/48 (43%)
Query: 421 VCARMNDKENFEVKPVKGLTWGHAAVGNATWTGARLVDVLKAAGISPD 468
VCA KE VK G WG A + WTG RL D+L G
Sbjct: 94 VCAGNRRKEQNMVKKTIGFNWGAAGTSTSLWTGVRLSDLLDRCGPKSP 141
Score = 40.1 bits (94), Expect = 0.004
Identities = 15/37 (40%), Positives = 23/37 (62%), Gaps = 2/37 (5%)
Query: 482 EIWSKAVDSSYNTQPESFANIWNLRGVLSNAYHRVRV 518
EI +A D S NTQP WN+ G+++N + RV++
Sbjct: 352 EICVRAWDESMNTQPRDM--TWNVMGMMNNCWFRVKI 386
Score = 32.4 bits (74), Expect = 1.1
Identities = 16/37 (43%), Positives = 25/37 (67%), Gaps = 2/37 (5%)
Query: 120 RSP-LLKATSLKPYNAEPPPSMLVEN-FLTPSLLSQV 154
R P L++ T P+N+EPP + L+++ F+TPS L V
Sbjct: 11 RDPRLIRLTGKHPFNSEPPLTELMDHGFITPSNLHYV 47
>gnl|CDD|201057 pfam00173, Cyt-b5, Cytochrome b5-like Heme/Steroid binding
domain. This family includes heme binding domains from
a diverse range of proteins. This family also includes
proteins that bind to steroids. The family includes
progesterone receptors. Many members of this subfamily
are membrane anchored by an N-terminal transmembrane
alpha helix. This family also includes a domain in some
chitin synthases. There is no known ligand for this
domain in the chitin synthases.
Length = 74
Score = 67.6 bits (166), Expect = 5e-14
Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 4/76 (5%)
Query: 23 YSLSDIQNHKDLKSSIWVVFRQGVYDITEFVQMHPGGE-IIMKAAGGSIEPFWAMYGVHL 81
++L +++ H + W+V VYD+T F++ HPGGE +I+ AAG +
Sbjct: 1 FTLEEVKKH-NKDGDCWIVINGKVYDVTRFLKDHPGGEDVILSAAGKDATEAFEDA--IH 57
Query: 82 QDEVFELLESYRIGNI 97
+ +LLE YR+G +
Sbjct: 58 SEAARKLLEKYRVGEL 73
>gnl|CDD|237339 PRK13299, PRK13299, tRNA CCA-pyrophosphorylase; Provisional.
Length = 394
Score = 73.3 bits (181), Expect = 1e-13
Identities = 38/141 (26%), Positives = 61/141 (43%), Gaps = 18/141 (12%)
Query: 649 DGTVYDYFNGHEDLKKGVCAFVGDPVSRIQEDYLRILRYFRFFARICNNPNNHK--EEVL 706
+G + D F+G EDLK + VG+ R QED LR++R RF +++ E
Sbjct: 124 NGEIIDLFDGLEDLKNRLIRAVGNAEERFQEDALRMMRAVRFASQL-----GFDLETETF 178
Query: 707 SAIKNNLDGLHNISGERIWTELNKILGGSFSKEMMLKMLYQNLLLFSKLKATTMREYIVE 766
A+K L IS ERI+ E K+L G F ++ + ++ T + Y+
Sbjct: 179 EAMKTQAPLLEKISVERIFVEFEKLLLGPFWRKGLKLLI-----------ETGLYNYLPG 227
Query: 767 LMKYKEKSELIKDFHKWRLPT 787
L +E + + T
Sbjct: 228 LKGKEENLLKLTQLLWFSFET 248
Score = 52.1 bits (126), Expect = 8e-07
Identities = 25/59 (42%), Positives = 37/59 (62%), Gaps = 6/59 (10%)
Query: 375 SIMDMLMGKKPHDIDFATNATPDQMKAMFAEEKVRTFNEKGEKHGTVCARMNDKENFEV 433
S+ D L+G+ HD+D AT+A P+++KA+F RT + G +HGTV N E +EV
Sbjct: 29 SVRDYLLGRPIHDVDIATSAYPEEVKAIFP----RTV-DVGIEHGTVLVLEN-GEEYEV 81
Score = 38.7 bits (91), Expect = 0.013
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 4/64 (6%)
Query: 811 EEVLSAIKKNLDGLHNISGERIWTELNKILGGSFSKEMMLKMLEINMFPHL----GTDET 866
E A+K L IS ERI+ E K+L G F ++ + ++E ++ +L G +E
Sbjct: 175 TETFEAMKTQAPLLEKISVERIFVEFEKLLLGPFWRKGLKLLIETGLYNYLPGLKGKEEN 234
Query: 867 FATL 870
L
Sbjct: 235 LLKL 238
Score = 30.6 bits (70), Expect = 4.0
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 898 ITTLRI-DVTTDGRH-AEVQFTEDWKLDANRRDLTVNSM 934
+TT R D R +EV F + D RRD T+N++
Sbjct: 81 VTTFRTESEYVDYRRPSEVTFVRSLEEDLKRRDFTINAI 119
>gnl|CDD|143388 cd05398, NT_ClassII-CCAase, Nucleotidyltransferase (NT) domain of
ClassII CCA-adding enzymes. CCA-adding enzymes add the
sequence [cytidine(C)-cytidine-adenosine (A)], one
nucleotide at a time, onto the 3' end of tRNA, in a
template-independent reaction. This Class II group is
comprised mainly of eubacterial and eukaryotic enzymes
and includes Bacillus stearothermophilus CCAase,
Escherichia coli poly(A) polymerase I, human
mitochondrial CCAase, and Saccharomyces cerevisiae
CCAase (CCA1). CCA-adding enzymes have a single
catalytic pocket, which recognizes both ATP and CTP
substrates. Included in this subgroup are CC- and
A-adding enzymes from various ancient species of
bacteria such as Aquifex aeolicus; these enzymes
collaborate to add CCA to tRNAs. This family belongs to
the Pol beta-like NT superfamily. In the majority of
enzymes in this superfamily, two carboxylates, Dx[D/E],
together with a third more distal carboxylate,
coordinate two divalent metal cations involved in a
two-metal ion mechanism of nucleotide addition. These
carboxylate residues are fairly well conserved in this
family. Escherichia coli CCAase is related to this group
but has not been included in this alignment as this
enzyme lacks the N-terminal helix conserved in the
remainder of the NT superfamily.
Length = 139
Score = 64.5 bits (158), Expect = 3e-12
Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 378 DMLMGKKPHDIDFATNA-TPDQMKAMFAEEKVRTFNEKGEKHGTVCARMNDKENFEV 433
D+L+G+ P DID AT+A P+ +A+F + R GE+ GT +N +V
Sbjct: 28 DLLLGRPPKDIDIATDADGPEFAEALFKKIGGRVVG-LGEEFGTATVVING-LTIDV 82
Score = 48.0 bits (115), Expect = 2e-06
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 4/41 (9%)
Query: 898 ITTLRIDVTTD--GRHAEVQFTEDWKLDANRRDLTVNSMFL 936
+ TLR + TD R V FT + D RRD T+N+M
Sbjct: 82 VATLRTETYTDPGRRPPVVGFTIE--EDLLRRDFTINAMAY 120
>gnl|CDD|216675 pfam01743, PolyA_pol, Poly A polymerase head domain. This family
includes nucleic acid independent RNA polymerases, such
as Poly(A) polymerase, which adds the poly (A) tail to
mRNA EC:2.7.7.19. This family also includes the tRNA
nucleotidyltransferase that adds the CCA to the 3' of
the tRNA EC:2.7.7.25. This family is part of the
nucleotidyltransferase superfamily.
Length = 126
Score = 62.7 bits (153), Expect = 1e-11
Identities = 18/56 (32%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 378 DMLMGKKPHDIDFATNATPDQMKAMFAEEKVRTFNEKGEKHGTVCARMNDKENFEV 433
D+L+G+ P D+D AT+A P+Q+ +F ++ E G++ GT+ ++ EV
Sbjct: 10 DLLLGRPPKDVDIATDAGPEQVATLFR-NRIIVHLESGKEFGTIHVLFGNQI-LEV 63
Score = 45.0 bits (107), Expect = 1e-05
Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 898 ITTLRID-VTTDGRHA-EVQFTEDWKLDANRRDLTVNSMF 935
+ T R + +D R+ +FT + D RRD T+N++
Sbjct: 63 VATFRTESDESDFRNPKSEEFTGTLEEDLKRRDFTINALA 102
Score = 29.9 bits (68), Expect = 2.4
Identities = 11/18 (61%), Positives = 12/18 (66%)
Query: 649 DGTVYDYFNGHEDLKKGV 666
DG V D F G +DLK GV
Sbjct: 107 DGEVIDPFGGIKDLKNGV 124
>gnl|CDD|215141 PLN02252, PLN02252, nitrate reductase [NADPH].
Length = 888
Score = 67.8 bits (166), Expect = 2e-11
Identities = 35/147 (23%), Positives = 65/147 (44%), Gaps = 24/147 (16%)
Query: 249 KVILSDHESTSHWQQNDYKGFSPSTDWDTVDFAKSPA--------IQELPVISAICLPVA 300
++I++ ES +++ D + D + A + I EL + S I P
Sbjct: 289 RIIVTTAESDNYYHYRDNRVLPSHVDAEL---ANAEGWWYKPEYIINELNINSVITTPAH 345
Query: 301 DAKLKLE----NHQMEVQGYAWSGGGKAIVRVDVTIDQGRTWHVANFTGQDSQAPLTRHW 356
D L + ++GYA+SGGG+ + RV+V++D G TW + + + ++W
Sbjct: 346 DEILPINASTTQRPYTMKGYAYSGGGRKVTRVEVSLDGGETWRLCDLDHPEKPTKYGKYW 405
Query: 357 GWTLWRATIPVDPKTKEVSIMDMLMGK 383
W W + +V ++D+L K
Sbjct: 406 CWCFW---------SLDVEVLDLLGAK 423
Score = 52.4 bits (126), Expect = 1e-06
Identities = 36/122 (29%), Positives = 58/122 (47%), Gaps = 16/122 (13%)
Query: 23 YSLSDIQNHKDLKSSIWVVFRQGVYDITEFVQMHPGG--EIIMKAAGGSIEPFWAMYGVH 80
Y++S+++ H + + S W+V VYD T F++ HPGG I++ A E F A +H
Sbjct: 520 YTMSEVRKH-NSEDSCWIVVHGHVYDCTRFLKDHPGGADSILINAGTDCTEEFDA---IH 575
Query: 81 LQDEVFELLESYRIGNISQEDSKLAAKDIASDPYVMEPVRSPLLKATSLKPYNAEPPPSM 140
D+ ++LE YRIG + + AS P+ + +T+ A P P
Sbjct: 576 -SDKAKKMLEDYRIGEL------VTTGAAASSSASSHPLSAI---STASALAAASPAPGR 625
Query: 141 LV 142
V
Sbjct: 626 PV 627
Score = 51.2 bits (123), Expect = 2e-06
Identities = 25/77 (32%), Positives = 29/77 (37%), Gaps = 7/77 (9%)
Query: 421 VCARMNDKENFEVKPVKGLTWGHAAVGNATWTGARLVDVLKAAGISPDQSLDSADVQHV- 479
VCA KE VK G WG A V + W G RL DVL+ G+ +V
Sbjct: 166 VCAGNRRKEQNMVKQTIGFNWGAAGVSTSVWRGVRLRDVLRRCGVMS----RKGGALNVC 221
Query: 480 --HVEIWSKAVDSSYNT 494
E S Y T
Sbjct: 222 FEGAEDLPGGGGSKYGT 238
Score = 45.4 bits (108), Expect = 1e-04
Identities = 24/61 (39%), Positives = 32/61 (52%), Gaps = 9/61 (14%)
Query: 482 EIWSKAVDSSYNTQPESFANIWNLRGVLSNAYHRVRVEIWSKAVDSS------YNTQPEN 535
EI +A D S NTQPE IWNL G+++N + RV+V + K + TQP N
Sbjct: 424 EIAVRAWDESMNTQPEKL--IWNLMGMMNNCWFRVKVNV-CKPHKGEIGLVFEHPTQPGN 480
Query: 536 G 536
Sbjct: 481 Q 481
Score = 30.4 bits (69), Expect = 6.1
Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 6/76 (7%)
Query: 82 QDEVFELLESYRIGNISQEDSKLAAKDIA-SDPYVMEPVRSP-LLKATSLKPYNAEPPPS 139
++ + + N+ E S + +D D ++ R P L++ T P+N EPP +
Sbjct: 48 DEDEADYEDLIVKENVEVEPSVVDPRDEGTPDEWIP---RHPSLVRLTGKHPFNCEPPLA 104
Query: 140 MLVEN-FLTPSLLSQV 154
L+E+ F+TP+ L V
Sbjct: 105 RLMEHGFITPAPLHYV 120
>gnl|CDD|221674 pfam12627, PolyA_pol_RNAbd, Probable RNA and SrmB- binding site of
polymerase A. This region encompasses much of the RNA
and SrmB binding motifs on polymerase A.
Length = 64
Score = 49.7 bits (120), Expect = 7e-08
Identities = 16/51 (31%), Positives = 25/51 (49%)
Query: 811 EEVLSAIKKNLDGLHNISGERIWTELNKILGGSFSKEMMLKMLEINMFPHL 861
E L+AI++ L IS ERI+ EL K+L + + E + +L
Sbjct: 6 PETLAAIRELAPLLKKISPERIFEELLKLLLSGHPSRGLELLRETGLLEYL 56
Score = 44.3 bits (106), Expect = 5e-06
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 703 EEVLSAIKNNLDGLHNISGERIWTELNKILGGSFSKEMMLKMLYQNLLL 751
E L+AI+ L IS ERI+ EL K+L L++L + LL
Sbjct: 6 PETLAAIRELAPLLKKISPERIFEELLKLLLSGHPSR-GLELLRETGLL 53
>gnl|CDD|227599 COG5274, CYB5, Cytochrome b involved in lipid metabolism [Energy
production and conversion / Lipid metabolism].
Length = 164
Score = 51.0 bits (122), Expect = 3e-07
Identities = 32/115 (27%), Positives = 50/115 (43%), Gaps = 22/115 (19%)
Query: 2 EDGVKALSKLRAGEPISTLPWYSLSDIQNHKDL-------------------KSSIWVVF 42
DG K +KL AG+ + L W SL +Q H D+ W+V
Sbjct: 13 SDGPKYTNKLYAGKDHAALDWDSL--VQEHADILNDESPKPITAEEVAKHNKSEDCWIVI 70
Query: 43 RQGVYDITEFVQMHPGGEIIMKAAGGSIEPFWAMYGVHLQDEVFELLESYRIGNI 97
VYD+++F+ HPGGE I+K G + A +H ++ LL+ + +
Sbjct: 71 NGKVYDVSQFLDEHPGGEDIIKDTAGK-DATKAFNFLHHSHQIGNLLKDVYVDQV 124
>gnl|CDD|238198 cd00321, SO_family_Moco, Sulfite oxidase (SO) family, molybdopterin
binding domain. This molybdopterin cofactor (Moco)
binding domain is found in a variety of oxidoreductases,
main members of this family are nitrate reductase (NR)
and sulfite oxidase (SO). SO catalyzes the terminal
reaction in the oxidative degradation of the
sulfur-containing amino acids cysteine and methionine.
Assimilatory NRs catalyze the reduction of nitrate to
nitrite which is subsequently converted to NH4+ by
nitrite reductase. Common features of all known members
of this family are that they contain one single pterin
cofactor and part of the coordination of the metal (Mo)
is a cysteine ligand of the protein and that they
catalyze the transfer of an oxygen to or from a lone
pair of electrons on the substrate.
Length = 156
Score = 47.9 bits (115), Expect = 3e-06
Identities = 18/45 (40%), Positives = 22/45 (48%), Gaps = 7/45 (15%)
Query: 438 GLTWGHAAVGNATWTGARLVDVLKAAGISPDQSLDSADVQHVHVE 482
G WG AV NA WTG L D+L+ AG P ++V E
Sbjct: 52 GNRWGGGAVSNAEWTGVPLRDLLEEAGPKP-------GARYVVFE 89
>gnl|CDD|130997 TIGR01942, pcnB, poly(A) polymerase. This model describes the pcnB
family of poly(A) polymerases (also known as plasmid
copy number protein). These enzymes sequentially add
adenosine nucleotides to the 3' end of RNAs, targeting
them for degradation by the cell. This was originally
described for anti-sense RNAs, but was later
demonstrated for mRNAs as well. Members of this family
are as yet limited to the gamma- and
beta-proteobacteria, with putative members in the
Chlamydiacae and spirochetes. This family has homology
to tRNA nucleotidyltransferase (cca).
Length = 410
Score = 49.4 bits (118), Expect = 6e-06
Identities = 28/85 (32%), Positives = 41/85 (48%), Gaps = 3/85 (3%)
Query: 648 LDGTVYDYFNGHEDLKKGVCAFVGDPVSRIQEDYLRILRYFRFFARICNNPNNHKEEVLS 707
+ DY G EDLK +GDP SR QED +R+LR RF ++ + E
Sbjct: 135 SREVIIDYVGGMEDLKNRRLRLIGDPRSRYQEDPVRMLRALRFSVKLEFTID---ESTAR 191
Query: 708 AIKNNLDGLHNISGERIWTELNKIL 732
I+ + L I R++ E+ K+L
Sbjct: 192 PIRESAPLLKGIPPARLFEEILKLL 216
Score = 37.9 bits (88), Expect = 0.021
Identities = 11/28 (39%), Positives = 21/28 (75%)
Query: 376 IMDMLMGKKPHDIDFATNATPDQMKAMF 403
+ D+L+G +P D D T+ATP++++ +F
Sbjct: 39 VRDLLLGIEPKDFDVVTSATPEEVRKLF 66
>gnl|CDD|236939 PRK11623, pcnB, poly(A) polymerase I; Provisional.
Length = 472
Score = 49.7 bits (119), Expect = 6e-06
Identities = 38/130 (29%), Positives = 62/130 (47%), Gaps = 12/130 (9%)
Query: 649 DGTVYDYFNGHEDLKKGVCAFVGDPVSRIQEDYLRILRYFRFFARICNNPNNHKEEVLSA 708
D TV DY G +DLK+GV +G+P +R +ED +R+LR RF A++ E
Sbjct: 181 DFTVRDYVGGMKDLKEGVIRLIGNPETRYREDPVRMLRAVRFAAKL---DMRISPETAEP 237
Query: 709 IKNNLDGLHNISGERIWTELNKILGGSFSKEMMLKM----LYQNLL-----LFSKLKATT 759
I L++I R++ E K+L + E + L+Q L F++ +
Sbjct: 238 IPRLATLLNDIPPARLFEESLKLLQAGYGYETYKLLCEYHLFQPLFPTITRYFTENGDSP 297
Query: 760 MREYIVELMK 769
M I +++K
Sbjct: 298 MERIIEQVLK 307
Score = 47.1 bits (112), Expect = 4e-05
Identities = 15/26 (57%), Positives = 21/26 (80%)
Query: 378 DMLMGKKPHDIDFATNATPDQMKAMF 403
D+L+GKKP D D TNATP+Q++ +F
Sbjct: 78 DLLLGKKPKDFDVTTNATPEQVRKLF 103
>gnl|CDD|239031 cd02113, bact_SoxC_Moco, bacterial SoxC is a member of the sulfite
oxidase (SO) family of molybdopterin binding domains.
SoxC is involved in oxidation of sulfur compounds during
chemolithothrophic growth. Together with SoxD, a small
c-type heme containing subunit, it forms a
hetrotetrameric sulfite dehydrogenase. This
molybdopterin cofactor (Moco) binding domain is found in
a variety of oxidoreductases, main members of this
family are nitrate reductase (NR) and sulfite oxidase
(SO). Common features of all known members of this
family are that they contain one single pterin cofactor
and part of the coordination of the metal (Mo) is a
cysteine ligand of the protein and that they catalyze
the transfer of an oxygen to or from a lone pair of
electrons on the substrate.
Length = 326
Score = 45.9 bits (109), Expect = 6e-05
Identities = 24/50 (48%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 312 EVQGYAWSGGGKAIVRVDVTIDQGRTWHVANFTGQDSQAPLTR---HWGW 358
E+ G AWSG G+ I RVDV+ D GRTW A G LTR W W
Sbjct: 228 EISGLAWSGRGR-IRRVDVSFDGGRTWQDARLEGPVLPKALTRFRLPWKW 276
Score = 31.2 bits (71), Expect = 2.4
Identities = 10/33 (30%), Positives = 17/33 (51%)
Query: 435 PVKGLTWGHAAVGNATWTGARLVDVLKAAGISP 467
P+ + H + + WTG L +L+ AG+ P
Sbjct: 76 PLPTAQYTHGMLSCSEWTGVPLSTLLEEAGVKP 108
>gnl|CDD|237338 PRK13298, PRK13298, tRNA CCA-pyrophosphorylase; Provisional.
Length = 417
Score = 43.6 bits (103), Expect = 4e-04
Identities = 29/104 (27%), Positives = 47/104 (45%), Gaps = 13/104 (12%)
Query: 633 RKLTLSVQDKDRSFRLDGTVYDYFNGHEDLKKGVCAFVGDPVSRIQEDYLRILRYFRFFA 692
R LT++ +D + G D F G +D++ + V + ED LR+LR RF A
Sbjct: 91 RDLTINAIAQDEN----GNYIDPFQGKKDIQLRLLRHVSES---FIEDPLRVLRVARFAA 143
Query: 693 RICNNPNNHKEEVLS----AIKNNLDGLHNISGERIWTELNKIL 732
+ + +E + +K + L ++ ERIW E K L
Sbjct: 144 LLVHLGFKIAKETMILMCIMVKKH--ELLYLTPERIWNETEKAL 185
>gnl|CDD|215768 pfam00174, Oxidored_molyb, Oxidoreductase molybdopterin binding
domain. This domain is found in a variety of
oxidoreductases. This domain binds to a molybdopterin
cofactor. Xanthine dehydrogenases, that also bind
molybdopterin, have essentially no similarity.
Length = 144
Score = 40.2 bits (95), Expect = 0.001
Identities = 14/29 (48%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 440 TWGHAAVGNATWTGARLVDVLKAAGISPD 468
W +GNA WTG L D+L+ AG PD
Sbjct: 39 NWS---IGNAEWTGVPLRDLLELAGPKPD 64
>gnl|CDD|182810 PRK10885, cca, multifunctional tRNA nucleotidyl
transferase/2'3'-cyclic
phosphodiesterase/2'nucleotidase/phosphatase; Reviewed.
Length = 409
Score = 41.0 bits (97), Expect = 0.002
Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 3/45 (6%)
Query: 649 DGTVYDYFNGHEDLKKGVCAFVGDPVSRIQEDYLRILRYFRFFAR 693
DG + D + G DL+ + V + ED LR+LR RF AR
Sbjct: 103 DGELIDPYGGQRDLEARLLRHVSPAFA---EDPLRVLRVARFAAR 144
>gnl|CDD|239032 cd02114, bact_SorA_Moco, sulfite:cytochrome c oxidoreductase
subunit A (SorA), molybdopterin binding domain. SorA is
involved in oxidation of sulfur compounds during
chemolithothrophic growth. Together with SorB, a small
c-type heme containing subunit, it forms a hetrodimer.
It is a member of the sulfite oxidase (SO) family of
molybdopterin binding domains. This molybdopterin
cofactor (Moco) binding domain is found in a variety of
oxidoreductases, main members of this family are nitrate
reductase (NR) and sulfite oxidase (SO). Common features
of all known members of this family are that they
contain one single pterin cofactor and part of the
coordination of the metal (Mo) is a cysteine ligand of
the protein and that they catalyze the transfer of an
oxygen to or from a lone pair of electrons on the
substrate.
Length = 367
Score = 38.6 bits (90), Expect = 0.014
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 436 VKGLTWGHAAVGNATWTGARLVDVLKAAGISP 467
V+G + A+GNA W G L VL AG+
Sbjct: 111 VQGAQLANGAMGNARWAGVPLKAVLAKAGVQD 142
Score = 32.5 bits (74), Expect = 1.2
Identities = 40/157 (25%), Positives = 61/157 (38%), Gaps = 23/157 (14%)
Query: 226 NAEPPPSML--YSSLLRIP------FCSHTGKVILSDHESTSHWQQNDYKGFSPSTDWDT 277
N EP P +L Y L +P + H + + D E W Y+ P
Sbjct: 184 NGEPLP-VLNGYPLRLVVPGFYATYWVKHLSHITVLDKEFDGFWASQAYR--IPDNADAG 240
Query: 278 VDFAKSPA----IQELPVISAICLPVADAKLKLENHQMEVQGYAWSGGGKAIVRVDVTID 333
V+ +P I V S I + + ++ ++G A+ GG I RVDV+ D
Sbjct: 241 VEPGTAPDRTAPINRFKVRSFITSL-ENGAIVAPAGELALRGIAFDGG-SGIRRVDVSAD 298
Query: 334 QGRTWHVANFTGQDSQAPLTRHWGWTLWRATIPVDPK 370
G +W A G D L R + + W+ T+ K
Sbjct: 299 GGDSWTQATL-GPD----LGR-FSFRGWKLTLDGVKK 329
>gnl|CDD|131739 TIGR02692, tRNA_CCA_actino, tRNA adenylyltransferase. The enzyme
tRNA adenylyltransferase, also called
tRNA-nucleotidyltransferase and CCA-adding enzyme, can
add or repair the required CCA triplet at the 3'-end of
tRNA molecules. Genes encoding tRNA include the CCA tail
in some but not all bacteria, and this enzyme may be
required for viability. Members of this family represent
a distinct clade within the larger family pfam01743
(tRNA nucleotidyltransferase/poly(A) polymerase family
protein). The example from Streptomyces coelicolor was
shown to act as a CCA-adding enzyme and not as a poly(A)
polymerase [Protein synthesis, tRNA and rRNA base
modification].
Length = 466
Score = 38.6 bits (90), Expect = 0.015
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 375 SIMDMLMGKKPHDIDFATNATPDQMKAMFAEEKVRTFNEKGEKHGTVCARMND 427
S+ D L+G+ HD+DF T+A P++ A+ + + G GTV A +
Sbjct: 36 SVRDALLGRLGHDLDFTTDARPEETLAILRPWADAVW-DTGIAFGTVGAEKDG 87
Score = 36.2 bits (84), Expect = 0.084
Identities = 17/38 (44%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 898 ITTLRIDV-TTDGRHAEVQFTEDWKLDANRRDLTVNSM 934
ITT R D R EV F + + D RRD TVN+M
Sbjct: 92 ITTFRSDSYDGTSRKPEVTFGDTLEGDLIRRDFTVNAM 129
Score = 35.5 bits (82), Expect = 0.14
Identities = 25/85 (29%), Positives = 38/85 (44%), Gaps = 3/85 (3%)
Query: 650 GTVYDYFNGHEDLKKGVCAFVGDPVSRIQEDYLRILRYFRFFARICNNPNNHKEEVLSAI 709
+D G +DL V P +D LR+LR RF +++ V +A+
Sbjct: 139 LEFHDPVGGLDDLLAKVLDTPATPEQSFGDDPLRMLRAARFVSQLGFEVAP---RVRAAM 195
Query: 710 KNNLDGLHNISGERIWTELNKILGG 734
D + IS ER+ EL+K+L G
Sbjct: 196 TEMADQIERISAERVRVELDKLLLG 220
>gnl|CDD|178739 PLN03198, PLN03198, delta6-acyl-lipid desaturase; Provisional.
Length = 526
Score = 38.1 bits (88), Expect = 0.022
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 23 YSLSDIQNHKDLKSSIWVVFRQGVYDITEFVQMHPGGEII 62
+ LS++ H + W+V + VYD+++F HPGG +I
Sbjct: 106 HLLSEVAAHNK-PNDCWIVIKNKVYDVSDFAAEHPGGSVI 144
>gnl|CDD|106256 PRK13296, PRK13296, tRNA CCA-pyrophosphorylase; Provisional.
Length = 360
Score = 34.2 bits (78), Expect = 0.32
Identities = 32/107 (29%), Positives = 53/107 (49%), Gaps = 19/107 (17%)
Query: 633 RKLTLSVQDKDRSFRLDGTVYDYFNGHEDLKKGVC-----AFVGDPVSRIQEDYLRILRY 687
R LT++ D+ + V D FNG DL+ + AF+ DP LR++R
Sbjct: 91 RDLTINSIAIDQ----NNKVIDPFNGQADLQNRILRHTSIAFIEDP--------LRVVRL 138
Query: 688 FRFFARICNNPNNHKEEVLSAIKNNLDG--LHNISGERIWTELNKIL 732
RF A++ N + +E+L+ IK + L++++ ER+ E K L
Sbjct: 139 ARFKAQLSNFNFSIAQEMLALIKELVKTGELNHLTRERLHIEFVKAL 185
>gnl|CDD|234743 PRK00390, leuS, leucyl-tRNA synthetase; Validated.
Length = 805
Score = 33.9 bits (79), Expect = 0.48
Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 15/77 (19%)
Query: 350 APLTRHWGWTLW----------RATIP-VDPK---TKEVSIMDMLMGKKPHDIDFATNAT 395
AP H LW A P D EV+I+ + GK I+ +A+
Sbjct: 707 APFAPHLAEELWEKLGHEGSIANAPWPTADEAALVEDEVTIVVQVNGKVRGKIEVPADAS 766
Query: 396 PDQMKAM-FAEEKVRTF 411
++++A+ A+EKV+ F
Sbjct: 767 KEEIEALALADEKVQKF 783
>gnl|CDD|178740 PLN03199, PLN03199, delta6-acyl-lipid desaturase-like protein;
Provisional.
Length = 485
Score = 32.3 bits (73), Expect = 1.2
Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 5/78 (6%)
Query: 23 YSLSDIQNHKDLKSSIWVVFRQGVYDITEFVQMHPGGEIIMKAAGGSIEPFWAMYGVHLQ 82
S +++ H + W++ + VYD++ + HPGG +I AG + +A + H
Sbjct: 26 ISWQEVKKHASPDDA-WIIHQNKVYDVSNWHD-HPGGAVIFTHAGDDMTDIFAAF--HAP 81
Query: 83 DEVFELLESYRIGNISQE 100
L++ + IG++ E
Sbjct: 82 GSQ-ALMKKFYIGDLIPE 98
>gnl|CDD|212580 cd11707, DHR2_DOCK1, Dock Homology Region 2, a GEF domain, of Class
A Dedicator of Cytokinesis 1. Dock1, also called
Dock180, is an atypical guanine nucleotide exchange
factor (GEF) that lacks the conventional Dbl homology
(DH) domain. As a GEF, it activates small GTPases by
exchanging bound GDP for free GTP. Dock1 interacts with
the scaffold protein Elmo and the resulting complex
functions upstream of Rac in many biological events
including phagocytosis of apoptotic cells, cell
migration and invasion. In the nervous system, it
mediates attractive responses to netrin-1 and thus,
plays a role in axon outgrowth and pathfinding. DOCK
proteins are divided into four classes (A-D) based on
sequence similarity and domain architecture; class A
includes Dock1, 2 and 5. All DOCKs contain two homology
domains: the DHR-1 (Dock homology region-1), also called
CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and
DHR-2 (also called CZH2 or Docker). The DHR-1 domain
binds phosphatidylinositol-3,4,5-triphosphate. This
alignment model represents the DHR-2 domain of Dock1,
which contains the catalytic GEF activity for Rac and/or
Cdc42. Class A DOCKs, like Dock1, are specific GEFs for
Rac and they contain an SH3 domain at the N-terminal
region and a PxxP motif at the C-terminus.
Length = 400
Score = 31.9 bits (72), Expect = 1.6
Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 14/87 (16%)
Query: 550 ARLLTRPPNPHSVRFKSGPDGKMKLDSPEFHSCFT--PELKRLAGIFEKHGYQLRIAGEG 607
ARLLT+ PN ++ S P +K S ++ CFT P L+ K
Sbjct: 159 ARLLTQFPNAEKMKTTSPPGDDIKNSSGQYIQCFTVKPLLELPPKFQNK----------- 207
Query: 608 TVTAKVLSYRNRREKEDRIGENQPFRK 634
V+ +++S+ E + R ++P RK
Sbjct: 208 PVSEQIVSFYRVNEVQ-RFQYSRPVRK 233
>gnl|CDD|139469 PRK13297, PRK13297, tRNA CCA-pyrophosphorylase; Provisional.
Length = 364
Score = 31.1 bits (70), Expect = 2.8
Identities = 24/94 (25%), Positives = 43/94 (45%), Gaps = 7/94 (7%)
Query: 650 GTVYDYFNGHEDLKKGVCAFVGDPVSRIQEDYLRILRYFRFFARICNNPNNHKEEVLSAI 709
G + D +G D++ V VG+ + ED +RILR RF AR + + E +
Sbjct: 115 GELVDPLDGVADVRARVLRHVGEAFA---EDPVRILRLGRFAARFGD--FSIAPETMQLC 169
Query: 710 KNNLDG--LHNISGERIWTELNKILGGSFSKEMM 741
+ ++ + ER+W E+++ L M+
Sbjct: 170 RRMVEAGEADALVPERVWKEVSRGLMAQAPSRML 203
>gnl|CDD|175999 cd04033, C2_NEDD4_NEDD4L, C2 domain present in the Human neural
precursor cell-expressed, developmentally down-regulated
4 (NEDD4) and NEDD4-like (NEDD4L/NEDD42). Nedd4 and
Nedd4-2 are two of the nine members of the Human Nedd4
family. All vertebrates appear to have both Nedd4 and
Nedd4-2 genes. They are thought to participate in the
regulation of epithelial Na+ channel (ENaC) activity.
They also have identical specificity for ubiquitin
conjugating enzymes (E2). Nedd4 and Nedd4-2 are
composed of a C2 domain, 2-4 WW domains, and a ubiquitin
ligase Hect domain. Their WW domains can bind PPxY (PY)
or LPSY motifs, and in vitro studies suggest that WW3
and WW4 of both proteins bind PY motifs in the key
substrates, with WW3 generally exhibiting higher
affinity. Most Nedd4 family members, especially Nedd4-2,
also have multiple splice variants, which might play
different roles in regulating their substrates. C2
domains fold into an 8-standed beta-sandwich that can
adopt 2 structural arrangements: Type I and Type II,
distinguished by a circular permutation involving their
N- and C-terminal beta strands. Many C2 domains are
Ca2+-dependent membrane-targeting modules that bind a
wide variety of substances including bind phospholipids,
inositol polyphosphates, and intracellular proteins.
Most C2 domain proteins are either signal transduction
enzymes that contain a single C2 domain, such as protein
kinase C, or membrane trafficking proteins which contain
at least two C2 domains, such as synaptotagmin 1.
However, there are a few exceptions to this including
RIM isoforms and some splice variants of piccolo/aczonin
and intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions.
Length = 133
Score = 29.6 bits (67), Expect = 3.8
Identities = 16/29 (55%), Positives = 17/29 (58%), Gaps = 8/29 (27%)
Query: 183 VKVMAGNISQEDSKLAAKDI--ASDPYVM 209
VKV+AG LA KDI ASDPYV
Sbjct: 4 VKVLAG------IDLAKKDIFGASDPYVK 26
>gnl|CDD|219970 pfam08689, Med5, Mediator complex subunit Med5. The mediator
complex is required for the expression of nearly all RNA
pol II dependent genes in Saccharomyces cerevisiae.
Deletion of the MED5 gene leads to increased
transcription of nuclear genes encoding components of
the oxidative phosphorylation machinery, and decreased
transcription of mitochondrial genes encoding components
of the same machinery. There is no orthologue from
pombe, and this subunit appears to be fungal specific.
Length = 977
Score = 30.2 bits (68), Expect = 6.1
Identities = 18/101 (17%), Positives = 26/101 (25%), Gaps = 15/101 (14%)
Query: 459 VLKAAGISPDQSLDSADVQHVHVEIWSKAVDSSYNTQPESFANIWNLRGVLSNAYHRVRV 518
VL + L + S + P A I L S Y + +
Sbjct: 723 VLNINARPLLKQLKKFRRRE----------PSRSDIDPILEALISKLSFSRSGNYSQKEL 772
Query: 519 EIWSKAVDSSYNTQ-----PENGHPSGYQPRATLQGARLLT 554
E W+ N P+ Y R L +L
Sbjct: 773 ESWTFHTTQPLNKWLTNSFWNLHSPTYYTHRQLLALIDILG 813
>gnl|CDD|233659 TIGR01967, DEAH_box_HrpA, ATP-dependent helicase HrpA. This model
represents HrpA, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria
and a few high-GC Gram-positive bacteria. HrpA is about
1300 amino acids long, while its paralog HrpB, also
uncharacterized, is about 800 amino acids long. Related
characterized eukarotic proteins are RNA helicases
associated with pre-mRNA processing [Unknown function,
Enzymes of unknown specificity].
Length = 1283
Score = 30.5 bits (69), Expect = 6.2
Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 185 VMAGNISQEDSKLAAKDIAS-DPYVMEPVRSPLLKATSLKPY 225
VMA + E SKL A+ +A +P +EPV L+K +P+
Sbjct: 654 VMAAELV-ETSKLYARLVAKIEPEWVEPVAGHLIKKNYFEPH 694
>gnl|CDD|223758 COG0686, Ald, Alanine dehydrogenase [Amino acid transport and
metabolism].
Length = 371
Score = 29.6 bits (67), Expect = 8.3
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 9/58 (15%)
Query: 291 VISAICLPVADA-KLKLENHQMEVQGYAWSGGGKAIVRVDVTIDQGRTWHVANFTGQD 347
VI A+ +P A A KL +++ V VDV IDQG + ++ T D
Sbjct: 235 VIGAVLIPGAKAPKLVTREMVKQMK--------PGSVIVDVAIDQGGCFETSHPTTHD 284
>gnl|CDD|187629 cd05371, HSD10-like_SDR_c, 17hydroxysteroid dehydrogenase type 10
(HSD10)-like, classical (c) SDRs. HSD10, also known as
amyloid-peptide-binding alcohol dehydrogenase (ABAD),
was previously identified as a L-3-hydroxyacyl-CoA
dehydrogenase, HADH2. In fatty acid metabolism, HADH2
catalyzes the third step of beta-oxidation, the
conversion of a hydroxyl to a keto group in the
NAD-dependent oxidation of L-3-hydroxyacyl CoA. In
addition to alcohol dehydrogenase and HADH2 activites,
HSD10 has steroid dehydrogenase activity. Although the
mechanism is unclear, HSD10 is implicated in the
formation of amyloid beta-petide in the brain (which is
linked to the development of Alzheimer's disease).
Although HSD10 is normally concentrated in the
mitochondria, in the presence of amyloid beta-peptide it
translocates into the plasma membrane, where it's action
may generate cytotoxic aldehydes and may lower estrogen
levels through its use of 17-beta-estradiol as a
substrate. HSD10 is a member of the SRD family, but
differs from other SDRs by the presence of two
insertions of unknown function. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH
numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 252
Score = 29.2 bits (66), Expect = 8.8
Identities = 12/47 (25%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 444 AAVGNATWTGARLVDVLKAAGISPDQSLDSADVQHVH-VEIWSKAVD 489
AA+ A RL V+ AGI+ + Q H +E++ + ++
Sbjct: 64 AALALAKAKFGRLDIVVNCAGIAVAAKTYNKKGQQPHSLELFQRVIN 110
>gnl|CDD|222962 PHA03036, PHA03036, DNA polymerase; Provisional.
Length = 1004
Score = 29.6 bits (67), Expect = 9.2
Identities = 26/117 (22%), Positives = 49/117 (41%), Gaps = 27/117 (23%)
Query: 723 RIWTEL-----NKILGGSFSKEMMLKMLYQNLLLFSKLKATTMREYIVELMKYKEKSELI 777
+I EL K+L +F E + +Y+NL++ SK K TT++ YI + S
Sbjct: 771 KIAKELERIINEKVLFDNFKIE--FEAVYKNLIMQSKKKYTTLK-YIAS---STDGSVPE 824
Query: 778 KD-------------FHKWRLPTFPMNGNIIRQFFARICNNPNNHKEEVLSAIKKNL 821
+ FHK+ + + + + N N ++L +++K+L
Sbjct: 825 RVNKGTSETRRDVSKFHKYMIKIYK---TRLLDMLSEGNMNSNQVCIDILRSLEKDL 878
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 0.134 0.402
Gapped
Lambda K H
0.267 0.0877 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 48,281,267
Number of extensions: 4785260
Number of successful extensions: 4101
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4076
Number of HSP's successfully gapped: 77
Length of query: 939
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 833
Effective length of database: 6,236,078
Effective search space: 5194652974
Effective search space used: 5194652974
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: 64 (28.2 bits)