RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4592
(197 letters)
>gnl|CDD|216573 pfam01564, Spermine_synth, Spermine/spermidine synthase. Spermine
and spermidine are polyamines. This family includes
spermidine synthase that catalyzes the fifth (last) step
in the biosynthesis of spermidine from arginine, and
spermine synthase.
Length = 240
Score = 254 bits (652), Expect = 1e-86
Identities = 101/173 (58%), Positives = 129/173 (74%)
Query: 21 KEFGTALILDGIIQCTEFDEFSYSEMIAFLPLCSHPNPKKVLIVGGGDGGVAREVLKHPS 80
K FG L+LDG +Q TE DEF Y EMIA +PLCSHPNPKKVLI+GGGDGG REV+KHPS
Sbjct: 39 KTFGKILVLDGRVQLTERDEFIYHEMIAHVPLCSHPNPKKVLIIGGGDGGALREVVKHPS 98
Query: 81 VESAYLVEIDNRVIEVSKKYLPGMAVGLSDPRLTVHVGDGFRFMSEHQQEFDVIITDSSD 140
VE LVEID +VIE SKK+LP +A G DPR+ V +GDGF+F+ ++ EFDVII DS+D
Sbjct: 99 VEKITLVEIDEKVIEFSKKFLPSLAGGFDDPRVKVVIGDGFKFLKDYLVEFDVIIVDSTD 158
Query: 141 PVGPAESLFQASYFELMSRALRPGGIVCSQAGTLWYSLDCVGNTLQHCASVFP 193
PVGPAE+LF +++L+ RAL+ G+ +QA + W L+ + N L++ VFP
Sbjct: 159 PVGPAENLFSKEFYDLLKRALKEDGVFVTQAESPWLHLELIINILKNGKKVFP 211
>gnl|CDD|215208 PLN02366, PLN02366, spermidine synthase.
Length = 308
Score = 257 bits (658), Expect = 1e-86
Identities = 99/200 (49%), Positives = 136/200 (68%), Gaps = 9/200 (4%)
Query: 2 GVSLSLQVEEPFYPSSSNRKE--------FGTALILDGIIQCTEFDEFSYSEMIAFLPLC 53
G + SL+VE+ + S+ ++ +G L+LDG+IQ TE DE +Y EMI LPLC
Sbjct: 28 GEAHSLKVEKVLFQGKSDFQDVLVFESATYGKVLVLDGVIQLTERDECAYQEMITHLPLC 87
Query: 54 SHPNPKKVLIVGGGDGGVAREVLKHPSVESAYLVEIDNRVIEVSKKYLPGMAVGLSDPRL 113
S PNPKKVL+VGGGDGGV RE+ +H SVE + EID VI+VSKK+ P +AVG DPR+
Sbjct: 88 SIPNPKKVLVVGGGDGGVLREIARHSSVEQIDICEIDKMVIDVSKKFFPDLAVGFDDPRV 147
Query: 114 TVHVGDGFRFMSEHQQE-FDVIITDSSDPVGPAESLFQASYFELMSRALRPGGIVCSQAG 172
+H+GDG F+ + +D II DSSDPVGPA+ LF+ +FE ++RALRPGG+VC+QA
Sbjct: 148 NLHIGDGVEFLKNAPEGTYDAIIVDSSDPVGPAQELFEKPFFESVARALRPGGVVCTQAE 207
Query: 173 TLWYSLDCVGNTLQHCASVF 192
++W +D + + + C F
Sbjct: 208 SMWLHMDLIEDLIAICRETF 227
>gnl|CDD|188048 TIGR00417, speE, spermidine synthase. the SpeE subunit of
spermidine synthase catalysesthe reaction (putrescine +
S-adenosylmethioninamine = spermidine +
5'-methylthioadenosine) and is involved in polyamine
biosynthesis and in the biosynthesis of spermidine from
arganine. The region between residues 77 and 120 of the
seed alignment is thought to be involved in binding to
decarboxylated SAM [Central intermediary metabolism,
Polyamine biosynthesis].
Length = 271
Score = 253 bits (648), Expect = 1e-85
Identities = 91/174 (52%), Positives = 125/174 (71%)
Query: 21 KEFGTALILDGIIQCTEFDEFSYSEMIAFLPLCSHPNPKKVLIVGGGDGGVAREVLKHPS 80
+ FG L+LDG++Q TE DEF Y EMI +PL +HPNPK VL++GGGDGGV REVLKH S
Sbjct: 36 EAFGNVLVLDGVVQTTERDEFIYHEMITHVPLFTHPNPKHVLVIGGGDGGVLREVLKHKS 95
Query: 81 VESAYLVEIDNRVIEVSKKYLPGMAVGLSDPRLTVHVGDGFRFMSEHQQEFDVIITDSSD 140
VESA LV+ID +VIE+S+KYLP +A DPR+ + + DGF+F+++ + FDVII DS+D
Sbjct: 96 VESATLVDIDEKVIELSRKYLPNLAGSYDDPRVKLVIDDGFKFLADTENTFDVIIVDSTD 155
Query: 141 PVGPAESLFQASYFELMSRALRPGGIVCSQAGTLWYSLDCVGNTLQHCASVFPR 194
PVGPAE+LF ++EL+ +AL P GI +Q+ + W L+ + + + FP
Sbjct: 156 PVGPAETLFTKEFYELLKKALNPDGIFVAQSESPWLQLELIIDLKRKLKEAFPI 209
>gnl|CDD|234843 PRK00811, PRK00811, spermidine synthase; Provisional.
Length = 283
Score = 252 bits (646), Expect = 4e-85
Identities = 93/174 (53%), Positives = 120/174 (68%), Gaps = 1/174 (0%)
Query: 21 KEFGTALILDGIIQCTEFDEFSYSEMIAFLPLCSHPNPKKVLIVGGGDGGVAREVLKHPS 80
EFG L LDG + TE DEF Y EM+ +PL +HPNPK+VLI+GGGDGG REVLKHPS
Sbjct: 40 PEFGRLLALDGCVMTTERDEFIYHEMMTHVPLFAHPNPKRVLIIGGGDGGTLREVLKHPS 99
Query: 81 VESAYLVEIDNRVIEVSKKYLPGMAVGL-SDPRLTVHVGDGFRFMSEHQQEFDVIITDSS 139
VE LVEID RV+EV +KYLP +A G DPR+ + +GDG +F++E + FDVII DS+
Sbjct: 100 VEKITLVEIDERVVEVCRKYLPEIAGGAYDDPRVELVIGDGIKFVAETENSFDVIIVDST 159
Query: 140 DPVGPAESLFQASYFELMSRALRPGGIVCSQAGTLWYSLDCVGNTLQHCASVFP 193
DPVGPAE LF ++E RAL+ GI +Q+G+ +Y D + + + VFP
Sbjct: 160 DPVGPAEGLFTKEFYENCKRALKEDGIFVAQSGSPFYQADEIKDMHRKLKEVFP 213
>gnl|CDD|223498 COG0421, SpeE, Spermidine synthase [Amino acid transport and
metabolism].
Length = 282
Score = 225 bits (576), Expect = 2e-74
Identities = 85/176 (48%), Positives = 122/176 (69%)
Query: 21 KEFGTALILDGIIQCTEFDEFSYSEMIAFLPLCSHPNPKKVLIVGGGDGGVAREVLKHPS 80
++FG L+LDG++Q TE DEF Y EM+A +PL +HPNPK+VLI+GGGDGG REVLKH
Sbjct: 40 EDFGKVLVLDGVVQLTERDEFIYHEMLAHVPLLAHPNPKRVLIIGGGDGGTLREVLKHLP 99
Query: 81 VESAYLVEIDNRVIEVSKKYLPGMAVGLSDPRLTVHVGDGFRFMSEHQQEFDVIITDSSD 140
VE +VEID VIE+++KYLP + G DPR+ + + DG F+ + +++FDVII DS+D
Sbjct: 100 VERITMVEIDPAVIELARKYLPEPSGGADDPRVEIIIDDGVEFLRDCEEKFDVIIVDSTD 159
Query: 141 PVGPAESLFQASYFELMSRALRPGGIVCSQAGTLWYSLDCVGNTLQHCASVFPRLH 196
PVGPAE+LF ++E RAL+ GI +QAG+ + + + ++ + VF +
Sbjct: 160 PVGPAEALFTEEFYEGCRRALKEDGIFVAQAGSPFLQDEEIALAYRNVSRVFSIVP 215
>gnl|CDD|178418 PLN02823, PLN02823, spermine synthase.
Length = 336
Score = 150 bits (382), Expect = 8e-45
Identities = 71/183 (38%), Positives = 99/183 (54%), Gaps = 15/183 (8%)
Query: 21 KEFGTALILDGIIQCTEFDEFSYSEMIAFLPLCSHPNPKKVLIVGGGDGGVAREVLKHPS 80
K FG LI+DG +Q E DEF Y E + L HPNPK V I+GGG+G AREVL+H +
Sbjct: 67 KPFGKVLIIDGKMQSAEADEFVYHESLVHPALLHHPNPKTVFIMGGGEGSTAREVLRHKT 126
Query: 81 VESAYLVEIDNRVIEVSKKYLPGMAVGLSDPRLTVHVGDGFRFMSEHQQEFDVIITDSSD 140
VE + +ID V++ +K+L D RL + + D + + ++FDVII D +D
Sbjct: 127 VEKVVMCDIDQEVVDFCRKHLTVNREAFCDKRLELIINDARAELEKRDEKFDVIIGDLAD 186
Query: 141 PV--GPAESLFQASYFELM-SRALRPGGIVCSQAG-------TLWYSLDCVGNTLQHCAS 190
PV GP L+ S++E + L PGGI +QAG +S + NTL+
Sbjct: 187 PVEGGPCYQLYTKSFYERIVKPKLNPGGIFVTQAGPAGILTHKEVFS--SIYNTLRQ--- 241
Query: 191 VFP 193
VF
Sbjct: 242 VFK 244
>gnl|CDD|235139 PRK03612, PRK03612, spermidine synthase; Provisional.
Length = 521
Score = 126 bits (320), Expect = 2e-34
Identities = 56/166 (33%), Positives = 93/166 (56%), Gaps = 7/166 (4%)
Query: 27 LILDGIIQCTEFDEFSYSEMIAFLPLCSHPNPKKVLIVGGGDGGVAREVLKHPSVESAYL 86
L L+G +Q + DE+ Y E + + + P++VL++GGGDG REVLK+P VE L
Sbjct: 267 LYLNGRLQFSSRDEYRYHEALVHPAMAASARPRRVLVLGGGDGLALREVLKYPDVEQVTL 326
Query: 87 VEIDNRVIEVSKKYLPGMAV---GLSDPRLTVHVGDGFRFMSEHQQEFDVIITDSSDPVG 143
V++D + E+++ A+ L DPR+TV D F ++ + ++FDVII D DP
Sbjct: 327 VDLDPAMTELARTSPALRALNGGALDDPRVTVVNDDAFNWLRKLAEKFDVIIVDLPDPSN 386
Query: 144 PAES-LFQASYFELMSRALRPGGIVCSQAGTLWY---SLDCVGNTL 185
PA L+ ++ L+ R L P G++ Q+ + ++ + + TL
Sbjct: 387 PALGKLYSVEFYRLLKRRLAPDGLLVVQSTSPYFAPKAFWSIEATL 432
>gnl|CDD|226713 COG4262, COG4262, Predicted spermidine synthase with an N-terminal
membrane domain [General function prediction only].
Length = 508
Score = 118 bits (297), Expect = 2e-31
Identities = 58/167 (34%), Positives = 93/167 (55%), Gaps = 7/167 (4%)
Query: 27 LILDGIIQCTEFDEFSYSEMIAFLPLCSHPNPKKVLIVGGGDGGVAREVLKHPSVESAYL 86
L LDG +Q + DE+ Y E + + L S + VL++GGGDG RE+LK+P VE L
Sbjct: 259 LYLDGGLQFSTRDEYRYHESLVYPALSSVRGARSVLVLGGGDGLALRELLKYPQVEQITL 318
Query: 87 VEIDNRVIEVSKKYLPGMAV---GLSDPRLTVHVGDGFRFMSEHQQEFDVIITDSSDPVG 143
V++D R+IE++ A+ SDPR+TV D F+++ FDV+I D DP
Sbjct: 319 VDLDPRMIELASHATVLRALNQGSFSDPRVTVVNDDAFQWLRTAADMFDVVIVDLPDPST 378
Query: 144 PAES-LFQASYFELMSRALRPGGIVCSQAGTLWYSLD---CVGNTLQ 186
P+ L+ ++ L+SR L G++ QAG+ +++ + T++
Sbjct: 379 PSIGRLYSVEFYRLLSRHLAETGLMVVQAGSPYFTPRVFWRIDATIK 425
>gnl|CDD|234961 PRK01581, speE, spermidine synthase; Validated.
Length = 374
Score = 85.0 bits (210), Expect = 1e-19
Identities = 57/173 (32%), Positives = 90/173 (52%), Gaps = 17/173 (9%)
Query: 27 LILDGIIQCTEFDEFSYSEMIAFLPLCSHPNPKKVLIVGGGDGGVAREVLKHPSVESAYL 86
L LD +Q + DE Y E + + +PK+VLI+GGGDG REVLK+ +V L
Sbjct: 120 LYLDKQLQFSSVDEQIYHEALVHPIMSKVIDPKRVLILGGGDGLALREVLKYETVLHVDL 179
Query: 87 VEIDNRVIEVSKKYLPGMAVGLS-----DPRLTVHVGDGFRFMSEHQQEFDVIITDSSDP 141
V++D +I +++ +P + V L+ D R+ VHV D F+S +DVII D DP
Sbjct: 180 VDLDGSMINMARN-VPEL-VSLNKSAFFDNRVNVHVCDAKEFLSSPSSLYDVIIIDFPDP 237
Query: 142 VGPAES-LFQASYFELMSRALRPGGIVCSQAGT------LWYSLDCVGNTLQH 187
S L+ + F ++ L G Q+ + +++S +GNT++H
Sbjct: 238 ATELLSTLYTSELFARIATFLTEDGAFVCQSNSPADAPLVYWS---IGNTIEH 287
>gnl|CDD|179854 PRK04457, PRK04457, spermidine synthase; Provisional.
Length = 262
Score = 70.8 bits (174), Expect = 5e-15
Identities = 38/131 (29%), Positives = 62/131 (47%), Gaps = 12/131 (9%)
Query: 40 EFSYSE-MIAFLPLCSHPNPKKVLIVGGGDGGVAREVLKH-PSVESAYLVEIDNRVIEVS 97
E +Y+ M+ FL P P+ +L +G G G +A+ + + P VEI+ +VI V+
Sbjct: 50 ELAYTRAMMGFLLFN--PRPQHILQIGLGGGSLAKFIYTYLPDTRQT-AVEINPQVIAVA 106
Query: 98 KK--YLPGMAVGLSDPRLTVHVGDGFRFMSEHQQEFDVIITDSSDPVGPAESLFQASYFE 155
+ LP + R V DG +++ H+ DVI+ D D G ++L +F+
Sbjct: 107 RNHFELPE-----NGERFEVIEADGAEYIAVHRHSTDVILVDGFDGEGIIDALCTQPFFD 161
Query: 156 LMSRALRPGGI 166
AL GI
Sbjct: 162 DCRNALSSDGI 172
>gnl|CDD|100107 cd02440, AdoMet_MTases, S-adenosylmethionine-dependent
methyltransferases (SAM or AdoMet-MTase), class I;
AdoMet-MTases are enzymes that use
S-adenosyl-L-methionine (SAM or AdoMet) as a substrate
for methyltransfer, creating the product
S-adenosyl-L-homocysteine (AdoHcy). There are at least
five structurally distinct families of AdoMet-MTases,
class I being the largest and most diverse. Within this
class enzymes can be classified by different substrate
specificities (small molecules, lipids, nucleic acids,
etc.) and different target atoms for methylation
(nitrogen, oxygen, carbon, sulfur, etc.).
Length = 107
Score = 60.1 bits (146), Expect = 3e-12
Identities = 32/111 (28%), Positives = 47/111 (42%), Gaps = 8/111 (7%)
Query: 60 KVLIVGGGDGGVAREVLKHPSVESAYLVEIDNRVIEVSKKYLPGMAVGLSDPRLTVHVGD 119
+VL +G G G +A + P V+I +E+++K A L + V GD
Sbjct: 1 RVLDLGCGTGALALALASGP-GARVTGVDISPVALELARK----AAAALLADNVEVLKGD 55
Query: 120 GFRFMSEHQQEFDVIITDSSDPVGPAESLFQASYFELMSRALRPGGIVCSQ 170
E + FDVII SDP A + E R L+PGG++
Sbjct: 56 AEELPPEADESFDVII---SDPPLHHLVEDLARFLEEARRLLKPGGVLVLT 103
>gnl|CDD|222295 pfam13659, Methyltransf_26, Methyltransferase domain. This family
contains methyltransferase domains.
Length = 117
Score = 52.4 bits (126), Expect = 3e-09
Identities = 24/114 (21%), Positives = 43/114 (37%), Gaps = 7/114 (6%)
Query: 58 PKKVLIVGGGDGGVAREVLKHPSVESAYLVEIDNRVIEVSKKYLPGMAVGLSDPRLTVHV 117
+VL G G G + VE+D ++++ L + PR+ V V
Sbjct: 1 GDRVLDPGAGSGAFLLAAARAGPDARVVGVELDPEAAALARRRLALAGL---APRVRVVV 57
Query: 118 GDGFRFMSEHQQEFDVIITD---SSDPVGPAESLFQASYF-ELMSRALRPGGIV 167
GD + FD+++ + P ++ F R L+PGG++
Sbjct: 58 GDARELLELPDGSFDLVLGNPPYGPRAGDPKDNRDLYDRFLAAALRLLKPGGVL 111
>gnl|CDD|134311 PRK00536, speE, spermidine synthase; Provisional.
Length = 262
Score = 52.2 bits (125), Expect = 2e-08
Identities = 20/95 (21%), Positives = 44/95 (46%), Gaps = 6/95 (6%)
Query: 44 SEMIAFLPLCSHPNPKKVLIVGGGDGGVAREVLKHPSVESAYLVEIDNRVIEVSKKYLPG 103
SE++A + C+ K+VLIV G D +A ++ K+ + V+ D ++++ + P
Sbjct: 59 SELLAHMGGCTKKELKEVLIVDGFDLELAHQLFKYDT--HVDFVQADEKILDSFISFFPH 116
Query: 104 MAVGLSDPRLTVHVGDGFRFMSEHQQEFDVIITDS 138
++ T + + +++D+II
Sbjct: 117 FHEVKNNKNFTHAK----QLLDLDIKKYDLIICLQ 147
>gnl|CDD|221804 pfam12847, Methyltransf_18, Methyltransferase domain. Protein in
this family function as methyltransferases.
Length = 104
Score = 39.2 bits (92), Expect = 1e-04
Identities = 21/110 (19%), Positives = 43/110 (39%), Gaps = 12/110 (10%)
Query: 58 PKKVLIVGGGDGGVAREVLKHPSVESAYLVEIDNRVIEVSKKYLPGMAVGLSDPRLTVHV 117
+VL +G G G +A E+ + V++ ++E++++ A PR+T
Sbjct: 2 GARVLDIGCGTGSLAIELARLFPGARVTGVDLSPEMLELARE----NAKLALGPRITFVQ 57
Query: 118 GDGFRFMSEHQQEFDVIITDSSDPVGPAESLFQASYFELMSRALRPGGIV 167
GD + + FD + + ++ L+PGG +
Sbjct: 58 GD-APDALDLLEGFDAVFIGGG-------GGDLLELLDALASLLKPGGRL 99
>gnl|CDD|219760 pfam08242, Methyltransf_12, Methyltransferase domain. Members of
this family are SAM dependent methyltransferases.
Length = 98
Score = 36.6 bits (85), Expect = 0.001
Identities = 23/111 (20%), Positives = 42/111 (37%), Gaps = 18/111 (16%)
Query: 62 LIVGGGDGGVAREVLKHPSVESAYLVEIDNRVIEVSKKYLPGMAVGLSDPRLTVHVGDGF 121
L +G G G + R +L+ V+I +E + + L L R+ + V D
Sbjct: 1 LDIGCGTGTLLRALLEALPGLEYTGVDISPAALEAAAERLAA-LGLLDAVRVRLDVLDAI 59
Query: 122 RFMSEHQQEFDVIITDSSDPVGPAESLFQA-----SYFELMSRALRPGGIV 167
FDV++ A ++ + + R L+PGG++
Sbjct: 60 ---DLDPGSFDVVV---------ASNVLHHLADPRAVLRNLRRLLKPGGVL 98
>gnl|CDD|225319 COG2521, COG2521, Predicted archaeal methyltransferase [General
function prediction only].
Length = 287
Score = 36.6 bits (85), Expect = 0.004
Identities = 33/127 (25%), Positives = 56/127 (44%), Gaps = 12/127 (9%)
Query: 59 KKVLIVGGGDGGVAREVLKHPSVESAYLVEIDNRVIEVSKKYLPGMAVGLSDPRLTVHVG 118
++VL G G A E L+ ++ VE D V+E++K L + L + + + +G
Sbjct: 136 ERVLDTCTGLGYTAIEALERGAIH-VITVEKDPNVLELAK--LNPWSRELFEIAIKIILG 192
Query: 119 DGFRFMSEHQQE-FDVIITDSSDP--VGPAESLFQASYFELMSRALRPGGIV---CSQAG 172
D + + + E FD II DP A L+ ++ + R L+ GG + G
Sbjct: 193 DAYEVVKDFDDESFDAII---HDPPRFSLAGELYSEEFYRELYRILKRGGRLFHYVGNPG 249
Query: 173 TLWYSLD 179
+ LD
Sbjct: 250 KRYRGLD 256
>gnl|CDD|216527 pfam01488, Shikimate_DH, Shikimate / quinate 5-dehydrogenase. This
family contains both shikimate and quinate
dehydrogenases. Shikimate 5-dehydrogenase catalyzes the
conversion of shikimate to 5-dehydroshikimate. This
reaction is part of the shikimate pathway which is
involved in the biosynthesis of aromatic amino acids.
Quinate 5-dehydrogenase catalyzes the conversion of
quinate to 5-dehydroquinate. This reaction is part of
the quinate pathway where quinic acid is exploited as a
source of carbon in prokaryotes and microbial
eukaryotes. Both the shikimate and quinate pathways
share two common pathway metabolites 3-dehydroquinate
and dehydroshikimate.
Length = 133
Score = 33.1 bits (76), Expect = 0.030
Identities = 24/91 (26%), Positives = 42/91 (46%), Gaps = 22/91 (24%)
Query: 59 KKVLIVGGGDGGVAREVLKHPSVESAYLVEIDNRVIE----VSKKYL-PGMAVGLSDPRL 113
KKVL++G G +AR KH + A + I NR +E +++++ G A+ L +
Sbjct: 13 KKVLLIGAG--EMARLAAKHLLSKGAKKITIANRTLEKAKELAEEFPVGGEALPLDE--- 67
Query: 114 TVHVGDGFRFMSEHQQEFDVII--TDSSDPV 142
+ E E D++I T + P+
Sbjct: 68 ----------LEELLAEADIVISATSAPTPI 88
>gnl|CDD|226607 COG4122, COG4122, Predicted O-methyltransferase [General function
prediction only].
Length = 219
Score = 33.8 bits (78), Expect = 0.033
Identities = 26/116 (22%), Positives = 45/116 (38%), Gaps = 17/116 (14%)
Query: 57 NPKKVLIVGGGDG----GVAREVLKHPSVESAYLVEIDNRVIEVSKKYLPGMAVGLSDPR 112
PK++L +G G +A + + +E D E++++ L G+ D
Sbjct: 59 GPKRILEIGTAIGYSALWMALALPDDGRL---TTIERDEERAEIARENLA--EAGVDDRI 113
Query: 113 LTVHVGDGFRFMSEHQQE-FDVIITDSSDPVGPAESLFQASYFELMSRALRPGGIV 167
+ GD +S FD++ D+ P Y E LRPGG++
Sbjct: 114 ELLLGGDALDVLSRLLDGSFDLVFIDADKADYPE-------YLERALPLLRPGGLI 162
>gnl|CDD|240373 PTZ00345, PTZ00345, glycerol-3-phosphate dehydrogenase;
Provisional.
Length = 365
Score = 33.8 bits (78), Expect = 0.036
Identities = 28/96 (29%), Positives = 38/96 (39%), Gaps = 25/96 (26%)
Query: 57 NPKKVLIVGGGDGGVA----------REVLKHPSV---------ESAYLVEIDNRVIEVS 97
P KV ++G G+ G A R + H V E L +I N E +
Sbjct: 10 GPLKVSVIGSGNWGSAISKVVGENTQRNYIFHNEVRMWVLEEIVEGEKLSDIINTKHE-N 68
Query: 98 KKYLPGMA-----VGLSDPRLTVHVGDGFRFMSEHQ 128
KYLPG+ V +SD + V D F+ HQ
Sbjct: 69 VKYLPGIKLPDNIVAVSDLKEAVEDADLLIFVIPHQ 104
>gnl|CDD|216840 pfam02005, TRM, N2,N2-dimethylguanosine tRNA methyltransferase.
This enzyme EC:2.1.1.32 used S-AdoMet to methylate tRNA.
The TRM1 gene of Saccharomyces cerevisiae is necessary
for the N2,N2-dimethylguanosine modification of both
mitochondrial and cytoplasmic tRNAs. The enzyme is found
in both eukaryotes and archaebacteria.
Length = 375
Score = 32.7 bits (75), Expect = 0.093
Identities = 27/99 (27%), Positives = 47/99 (47%), Gaps = 17/99 (17%)
Query: 73 REVLKHPSVESAYLVEIDNRVIEVSKKYLPGMAVGLSD--PRLTVHVGDGFRFMSEHQQE 130
R L+ P VE + +I + +E+ K+ V L++ + ++ D M E+ +
Sbjct: 66 RFALEVPGVEEVFANDISPKAVELIKE-----NVKLNEVENIVVINGDDANMLMRENHRR 120
Query: 131 FDVIITDSSDPVG-PAESLFQASYFELMSRALRPGGIVC 168
FDVI DP G PA L A ++++ GG++C
Sbjct: 121 FDVI---DLDPFGSPAPFLDSA------VQSVKRGGLLC 150
>gnl|CDD|128898 smart00650, rADc, Ribosomal RNA adenine dimethylases.
Length = 169
Score = 31.7 bits (73), Expect = 0.14
Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 12/65 (18%)
Query: 61 VLIVGGGDGGVAREVLKHPSVESAYL--VEIDNRVIEVSKKYLPGMAVGLSDPRLTVHVG 118
VL +G G G + E+L+ + + +EID R+ ++ LTV G
Sbjct: 17 VLEIGPGKGALTEELLER----AKRVTAIEIDPRLAPRLREKFAA------ADNLTVIHG 66
Query: 119 DGFRF 123
D +F
Sbjct: 67 DALKF 71
>gnl|CDD|216177 pfam00891, Methyltransf_2, O-methyltransferase. This family
includes a range of O-methyltransferases. These enzymes
utilise S-adenosyl methionine.
Length = 239
Score = 31.1 bits (71), Expect = 0.27
Identities = 14/61 (22%), Positives = 23/61 (37%), Gaps = 15/61 (24%)
Query: 64 VGGGDGGVAREVL-KHPSVESAYLVEIDNRVIEVSKKYLPGMAVGLSD-PRLTVHVGDGF 121
VGGG G +A ++ +P ++ + D LP + R+ GD F
Sbjct: 108 VGGGTGALAAAIVRAYPHIK---GIVFD----------LPHVIADAPSADRVEFVGGDFF 154
Query: 122 R 122
Sbjct: 155 E 155
>gnl|CDD|223450 COG0373, HemA, Glutamyl-tRNA reductase [Coenzyme metabolism].
Length = 414
Score = 30.7 bits (70), Expect = 0.43
Identities = 25/89 (28%), Positives = 40/89 (44%), Gaps = 20/89 (22%)
Query: 59 KKVLIVGGGDGGVAREVLKHPSVESAYLVEIDNRVIEVSK---KYLPGMAVGLSDPRLTV 115
KKVL++G G+ + V KH + + + I NR +E ++ K L AV L +
Sbjct: 179 KKVLVIGAGE--MGELVAKHLAEKGVKKITIANRTLERAEELAKKLGAEAVALEE----- 231
Query: 116 HVGDGFRFMSEHQQEFDVII--TDSSDPV 142
+ E E DV+I T + P+
Sbjct: 232 --------LLEALAEADVVISSTSAPHPI 252
>gnl|CDD|225370 COG2813, RsmC, 16S RNA G1207 methylase RsmC [Translation, ribosomal
structure and biogenesis].
Length = 300
Score = 30.3 bits (69), Expect = 0.59
Identities = 25/119 (21%), Positives = 47/119 (39%), Gaps = 30/119 (25%)
Query: 59 KKVLIVGGGDGGVAREVLKHPSVESAYLVEIDNRVIEVSKKYLPGMAVGLSDPRLTVHVG 118
KVL +G G G + + K LV+++ R +E ++K L+ +
Sbjct: 160 GKVLDLGCGYGVLGLVLAKKSPQAKLTLVDVNARAVESARK-------NLAANGVE---- 208
Query: 119 DGFRFMSEHQQ----EFDVIIT--------DSSDPVGPAESLFQASYFELMSRALRPGG 165
+ + S + +FD+II+ + A+ + A+ R L+PGG
Sbjct: 209 NTEVWASNLYEPVEGKFDLIISNPPFHAGKAVVHSL--AQEIIAAAA-----RHLKPGG 260
>gnl|CDD|224780 COG1867, TRM1, N2,N2-dimethylguanosine tRNA methyltransferase
[Translation, ribosomal structure and biogenesis].
Length = 380
Score = 30.4 bits (69), Expect = 0.64
Identities = 19/55 (34%), Positives = 25/55 (45%), Gaps = 10/55 (18%)
Query: 115 VHVGDGFRFMSEHQQEFDVIITDSSDPVG-PAESLFQASYFELMSRALRPGGIVC 168
V D + E + FDVI DP G PA L A R++R GG++C
Sbjct: 106 VINKDANALLHELHRAFDVI---DIDPFGSPAPFLDAA------LRSVRRGGLLC 151
>gnl|CDD|224172 COG1252, Ndh, NADH dehydrogenase, FAD-containing subunit [Energy
production and conversion].
Length = 405
Score = 30.3 bits (69), Expect = 0.64
Identities = 16/71 (22%), Positives = 32/71 (45%), Gaps = 5/71 (7%)
Query: 56 PNPKKVLIVGGGDGGV--AREVLKHPSVESAYLVEIDNRVIEVSKKYLPGMAVG-LSDPR 112
K+++I+GGG GG+ A+ + + + +D R + L +A G LS+
Sbjct: 1 MMKKRIVILGGGFGGLSAAKRLARKL--PDVEITLVDRRDYHLFTPLLYEVATGTLSESE 58
Query: 113 LTVHVGDGFRF 123
+ + + R
Sbjct: 59 IAIPLRALLRK 69
Score = 27.2 bits (61), Expect = 6.2
Identities = 22/111 (19%), Positives = 34/111 (30%), Gaps = 18/111 (16%)
Query: 11 EPFYPSSSNRKEFGTALILDGIIQCTEFDE--FSYSEMIAFLPLCSHPNPKKVLIVGGGD 68
E Y E+ A L + E + ++IVGGG
Sbjct: 110 ETNYFGIPGAAEY--AFGLKTLEDALRLRRHLLEAFEKASQEE--DDRALLTIVIVGGGP 165
Query: 69 GGV---------AREVLKHPSVESAYLVEIDNRVIEVSKKYLPGMAVGLSD 110
GV +LK V+ + E+ ++E + LP LS
Sbjct: 166 TGVELAGELAERLHRLLKKFRVDPS---ELRVILVEAGPRILPMFPPKLSK 213
>gnl|CDD|224562 COG1648, CysG, Siroheme synthase (precorrin-2
oxidase/ferrochelatase domain) [Coenzyme metabolism].
Length = 210
Score = 30.0 bits (68), Expect = 0.69
Identities = 21/97 (21%), Positives = 40/97 (41%), Gaps = 16/97 (16%)
Query: 46 MIAFLPLCSHPNPKKVLIVGGGDGGVAREVLKHPSVESAYLVEIDNRVIEVSKKYLPGMA 105
+ FL L KKVL+VGGG + + L L++ V VS ++ P +
Sbjct: 4 LPLFLDL----EGKKVLVVGGGSVALRKARL---------LLKAGADVTVVSPEFEPELK 50
Query: 106 VGLSDPRLTVHVGDGFRFMSEHQQEFDVIITDSSDPV 142
+ + ++ + F +E + ++I + D
Sbjct: 51 ALIEEGKIKWIERE---FDAEDLDDAFLVIAATDDEE 84
>gnl|CDD|235874 PRK06847, PRK06847, hypothetical protein; Provisional.
Length = 375
Score = 29.8 bits (68), Expect = 0.88
Identities = 17/36 (47%), Positives = 23/36 (63%), Gaps = 2/36 (5%)
Query: 56 PNPKKVLIVGGGDGGVAREV-LKHPSVESAYLVEID 90
KKVLIVGGG GG++ + L+ + + LVEID
Sbjct: 2 AAVKKVLIVGGGIGGLSAAIALRRAGI-AVDLVEID 36
>gnl|CDD|223109 COG0030, KsgA, Dimethyladenosine transferase (rRNA methylation)
[Translation, ribosomal structure and biogenesis].
Length = 259
Score = 29.5 bits (67), Expect = 0.89
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 8/63 (12%)
Query: 61 VLIVGGGDGGVAREVLKHPSVESAYLVEIDNRVIEVSKKYLPGMAVGLSDPRLTVHVGDG 120
VL +G G G + +L+ + +A +EID R+ EV K+ LTV GD
Sbjct: 34 VLEIGPGLGALTEPLLERAARVTA--IEIDRRLAEVLKERFA------PYDNLTVINGDA 85
Query: 121 FRF 123
+F
Sbjct: 86 LKF 88
>gnl|CDD|236630 PRK09853, PRK09853, putative selenate reductase subunit YgfK;
Provisional.
Length = 1019
Score = 29.9 bits (68), Expect = 0.93
Identities = 13/31 (41%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 59 KKVLIVGGGDGG--VAREVLKHPSVESAYLV 87
K V++VGGG+ AR L+ P VE +V
Sbjct: 669 KHVVVVGGGNTAMDAARAALRVPGVEKVTVV 699
>gnl|CDD|133452 cd05213, NAD_bind_Glutamyl_tRNA_reduct, NADP-binding domain of
glutamyl-tRNA reductase. Glutamyl-tRNA reductase
catalyzes the conversion of glutamyl-tRNA to
glutamate-1-semialdehyde, initiating the synthesis of
tetrapyrrole. Whereas tRNAs are generally associated
with peptide bond formation in protein translation, here
the tRNA activates glutamate in the initiation of
tetrapyrrole biosynthesis in archaea, plants and many
bacteria. In the first step, activated glutamate is
reduced to glutamate-1-semi-aldehyde via the NADPH
dependent glutamyl-tRNA reductase. Glutamyl-tRNA
reductase forms a V-shaped dimer. Each monomer has 3
domains: an N-terminal catalytic domain, a classic
nucleotide binding domain, and a C-terminal dimerization
domain. Although the representative structure 1GPJ lacks
a bound NADPH, a theoretical binding pocket has been
described. (PMID 11172694). Amino acid dehydrogenase
(DH)-like NAD(P)-binding domains are members of the
Rossmann fold superfamily and include glutamate,
leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 311
Score = 29.5 bits (67), Expect = 1.0
Identities = 24/86 (27%), Positives = 38/86 (44%), Gaps = 18/86 (20%)
Query: 59 KKVLIVGGGDGGVAREVLKHPSVESAYLVEIDNRVIEVSK---KYLPGMAVGLSDPRLTV 115
KKVL++G G+ + KH + + + I NR E ++ K L G AV L +
Sbjct: 179 KKVLVIGAGE--MGELAAKHLAAKGVAEITIANRTYERAEELAKELGGNAVPLDE----- 231
Query: 116 HVGDGFRFMSEHQQEFDVIITDSSDP 141
+ E E DV+I+ + P
Sbjct: 232 --------LLELLNEADVVISATGAP 249
>gnl|CDD|239057 cd02143, NADH_nitroreductase, Nitroreductase family. Members of
this family utilize FMN as a cofactor. This family is
involved in the reduction of flavin or nitroaromatic
compounds by using NAD(P)H as electron donor in a
obligatory two-electron transfer. Nitrogenase is
homodimer. Each subunit contains one FMN molecule.
Members of this family are also called NADH
dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or
dihydropteridine reductase.
Length = 147
Score = 28.4 bits (64), Expect = 1.3
Identities = 15/64 (23%), Positives = 25/64 (39%), Gaps = 14/64 (21%)
Query: 133 VIITDSSDPVGPAESLFQASYFELMSRALRPGGIVCSQAGTLWYSLDCVGNTLQHCASVF 192
+ P +++ +YFEL ++AL G+ GT W Q A ++
Sbjct: 65 LASAPRDFPTAQVDAIIALTYFELAAQAL---GL-----GTCWAGF------FQAAAELY 110
Query: 193 PRLH 196
P L
Sbjct: 111 PPLR 114
>gnl|CDD|176037 cd08391, C2A_C2C_Synaptotagmin_like, C2 domain first and third
repeat in Synaptotagmin-like proteins. Synaptotagmin is
a membrane-trafficking protein characterized by a
N-terminal transmembrane region, a linker, and 2
C-terminal C2 domains. Previously all synaptotagmins
were thought to be calcium sensors in the regulation of
neurotransmitter release and hormone secretion, but it
has been shown that not all of them bind calcium. Of
the 17 identified synaptotagmins only 8 bind calcium
(1-3, 5-7, 9, 10). The function of the two C2 domains
that bind calcium are: regulating the fusion step of
synaptic vesicle exocytosis (C2A) and binding to
phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the
absence of calcium ions and to phosphatidylinositol
bisphosphate (PIP2) in their presence (C2B). C2B also
regulates also the recycling step of synaptic vesicles.
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. This cd contains either the
first or third repeat in Synaptotagmin-like proteins
with a type-I topology.
Length = 121
Score = 28.4 bits (64), Expect = 1.4
Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 10/50 (20%)
Query: 99 KYLPGMAVGLSDPRLTVHVGDGFRFMSEHQQE---------FDVIITDSS 139
K++ G+ G SDP + V VG F S+ +E ++ ++ +
Sbjct: 18 KFVGGLVKGKSDPYVIVRVG-AQTFKSKVIKENLNPKWNEVYEAVVDEVP 66
>gnl|CDD|203249 pfam05430, Methyltransf_30, S-adenosyl-L-methionine-dependent
methyltransferase. This family is a
S-adenosyl-L-methionine (SAM)-dependent
methyltransferase. It is often found in association with
pfam01266, where it is responsible for catalyzing the
transfer of a methyl group from S-adenosyl-L-methionine
to 5-aminomethyl-2-thiouridine to form
5-methylaminomethyl-2-thiouridine.
Length = 124
Score = 28.0 bits (63), Expect = 1.5
Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 3/59 (5%)
Query: 112 RLTVHVGDGFRFMSEHQQEFDVIITDS-SDPVGPAESLFQASYFELMSRALRPGGIVCS 169
L + GD + E + D D S P ++ +F L++R +PGG + +
Sbjct: 32 TLDLWFGDARAALPELDFKADAWFLDGFSPAKNPE--MWTEEFFALLARRSKPGGTLAT 88
>gnl|CDD|225151 COG2242, CobL, Precorrin-6B methylase 2 [Coenzyme metabolism].
Length = 187
Score = 28.7 bits (65), Expect = 1.5
Identities = 27/120 (22%), Positives = 43/120 (35%), Gaps = 14/120 (11%)
Query: 56 PNPKKVLI-VGGGDGGVAREVLKHPSVESAYLVEIDNRVIEVSKKYLPGMAVGLSDPRLT 114
P P L +G G G + E +E D +E+ ++ A L
Sbjct: 32 PRPGDRLWDIGAGTGSITIEWALAGPSGRVIAIERDEEALELIERN----AARFGVDNLE 87
Query: 115 VHVGDGFRFMSEHQQEFDVIITDSSDPVGPAESLFQASYFELMSRALRPGGIVCSQAGTL 174
V GD + + D I G E + +A++ L+PGG + + A TL
Sbjct: 88 VVEGDAPEALPD-LPSPDAIFIGGG---GNIEEILEAAW-----ERLKPGGRLVANAITL 138
>gnl|CDD|132434 TIGR03393, indolpyr_decarb, indolepyruvate decarboxylase, Erwinia
family. A family of closely related, thiamine
pyrophosphate-dependent enzymes includes indolepyruvate
decarboxylase (EC 4.1.1.74), phenylpyruvate
decarboxylase (EC 4.1.1.43), pyruvate decarboxylase (EC
4.1.1.1), branched-chain alpha-ketoacid decarboxylase,
etc.. Members of this group of homologs may overlap in
specificity. Within the larger family, this model
represents a clade of bacterial indolepyruvate
decarboxylases, part of a pathway for biosynthesis of
the plant hormone indole-3-acetic acid. Typically, these
species interact with plants, as pathogens or as
beneficial, root-associated bacteria [Central
intermediary metabolism, Other].
Length = 539
Score = 29.1 bits (65), Expect = 1.6
Identities = 10/39 (25%), Positives = 18/39 (46%)
Query: 135 ITDSSDPVGPAESLFQASYFELMSRALRPGGIVCSQAGT 173
P +L Q ++++ + LRPG I+ + GT
Sbjct: 343 AIPFPQPDESRSALSQENFWQTLQTFLRPGDIILADQGT 381
>gnl|CDD|226864 COG4457, SrfB, Uncharacterized protein conserved in bacteria,
putative virulence factor [Function unknown].
Length = 1014
Score = 29.0 bits (65), Expect = 2.1
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 137 DSSDPVGPAESLFQASYFELMSRALRPGGI 166
++ DP + AS+ EL+ RA R G I
Sbjct: 687 ENLDPTDHKAEIRAASFGELLGRAGRDGEI 716
>gnl|CDD|233708 TIGR02072, BioC, biotin biosynthesis protein BioC. This enzyme,
which is found in biotin biosynthetic gene clusters in
proteobacteria, firmicutes, green-sulfur bacteria,
fusobacterium and bacteroides, is believed to carry out
an enzymatic step prior to the formation of pimeloyl-CoA
(although attribution of this annotation is not
traceable). The enzyme appears related to
methyltransferases by homology [Biosynthesis of
cofactors, prosthetic groups, and carriers, Biotin].
Length = 240
Score = 28.4 bits (64), Expect = 2.1
Identities = 26/133 (19%), Positives = 47/133 (35%), Gaps = 31/133 (23%)
Query: 45 EMIAFLPLCSHPNPKKVLIVGGGDGGVAREVLKHPSVESAYLVEIDNRVIEVSKKYLPGM 104
++A L P VL +G G G + R +LK +I ++ +K L
Sbjct: 22 RLLALLKEKGIFIPASVLDIGCGTGYLTRALLKRFPQAEFIANDISAGMLAQAKTKLS-- 79
Query: 105 AVGLSDPRLTVHVGDGFRFMSEHQ----QEFDVIITDSSDPVGPAESLFQ-----ASYFE 155
+ GD E FD+I+++ + Q +
Sbjct: 80 ------ENVQFICGDA-----EKLPLEDSSFDLIVSNLA---------LQWCDDLSQALS 119
Query: 156 LMSRALRPGGIVC 168
++R L+PGG++
Sbjct: 120 ELARVLKPGGLLA 132
>gnl|CDD|235211 PRK04042, rpl4lp, 50S ribosomal protein L4P; Provisional.
Length = 254
Score = 28.3 bits (64), Expect = 2.4
Identities = 21/59 (35%), Positives = 27/59 (45%), Gaps = 12/59 (20%)
Query: 58 PKKVLIVGGGDGGVAREVLKHPSVESAYLVEIDNRVIEVSKKYL-PGMAVGLSDPRLTV 115
PK VLIV D + + P V+ +V +DN +E L PG G RLTV
Sbjct: 193 PKSVLIVVSDDSPIVKAARNLPGVD---VVTVDNLNVEH----LAPGGHPG----RLTV 240
>gnl|CDD|226906 COG4529, COG4529, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 474
Score = 28.5 bits (64), Expect = 2.4
Identities = 21/77 (27%), Positives = 30/77 (38%), Gaps = 10/77 (12%)
Query: 59 KKVLIVGGGDGGV--AREVLKHPSVESAYLVEIDNRVIEVSKKYLPGMAVGLSDP--RLT 114
KV I+GGG G+ A +LK P L+ I + G+A +P L
Sbjct: 2 FKVAIIGGGFSGIYMAAHLLKSPRPSG--LISIFEPRPNFGQ----GIAYSTEEPEHLLN 55
Query: 115 VHVGDGFRFMSEHQQEF 131
V F + Q+F
Sbjct: 56 VPAARMSAFAPDIPQDF 72
>gnl|CDD|235607 PRK05785, PRK05785, hypothetical protein; Provisional.
Length = 226
Score = 28.1 bits (63), Expect = 2.8
Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 5/42 (11%)
Query: 49 FLPLCSHPNPKKVLIVGGGDGGVAREVLKHPSVESAYLVEID 90
L C PKKVL V G G ++ K V Y+V +D
Sbjct: 45 ILKYC--GRPKKVLDVAAGKGELSY-HFK--KVFKYYVVALD 81
>gnl|CDD|222415 pfam13847, Methyltransf_31, Methyltransferase domain. This family
appears to be have methyltransferase activity.
Length = 151
Score = 27.8 bits (62), Expect = 2.8
Identities = 27/119 (22%), Positives = 44/119 (36%), Gaps = 17/119 (14%)
Query: 58 PKKVLIVGGGDGG----VAREVLKHPSVESAYLVEIDNRVIEVSKKYLPGMAVGLSDPRL 113
KVL +G G G +A ++ V ++I IE +K+ A L +
Sbjct: 4 GIKVLDLGCGTGYLTFILAEKLGPGAEV---VGIDISEEAIEKAKE----NAKKLGYENV 56
Query: 114 TVHVGDGFRF--MSEHQQEFDVIITDSSDPVGPAESLFQASYFELMSRALRPGGIVCSQ 170
GD + FDV+I++ P E + R L+PGG++
Sbjct: 57 EFIQGDIEELPQLQLEDNSFDVVISNEVLNHLPD----PDKVLEEIIRVLKPGGVLIVS 111
>gnl|CDD|187628 cd05370, SDR_c2, classical (c) SDR, subgroup 2. Short-chain
dehydrogenases/reductases (SDRs, aka Tyrosine-dependent
oxidoreductases) 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 = 228
Score = 27.7 bits (62), Expect = 3.2
Identities = 10/36 (27%), Positives = 14/36 (38%), Gaps = 8/36 (22%)
Query: 59 KKVLIVGGGDGGVAREVLKHPSVESAYLVEIDNRVI 94
VLI GG G+ + + +E N VI
Sbjct: 6 NTVLITGGT-SGIGLALAR-------KFLEAGNTVI 33
>gnl|CDD|233597 TIGR01850, argC, N-acetyl-gamma-glutamyl-phosphate reductase,
common form. This model represents the more common of
two related families of
N-acetyl-gamma-glutamyl-phosphate reductase, an enzyme
catalyzing the third step or Arg biosynthesis from Glu.
The two families differ by phylogeny, similarity
clustering, and the gap architecture in a multiple
sequence alignment. Bacterial members of this family
tend to be found within Arg biosynthesis operons [Amino
acid biosynthesis, Glutamate family].
Length = 346
Score = 27.9 bits (63), Expect = 3.5
Identities = 16/32 (50%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 59 KKVLIVGG-GDGGV--AREVLKHPSVESAYLV 87
KV IVG G G R +L HP VE YLV
Sbjct: 1 IKVAIVGASGYTGGELLRLLLNHPEVEITYLV 32
>gnl|CDD|237198 PRK12771, PRK12771, putative glutamate synthase (NADPH) small
subunit; Provisional.
Length = 564
Score = 27.9 bits (63), Expect = 3.7
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 50 LPLCSHPNPKKVLIVGGGDGG 70
P + K+V ++GGG G
Sbjct: 129 FPAPAPDTGKRVAVIGGGPAG 149
>gnl|CDD|222002 pfam13241, NAD_binding_7, Putative NAD(P)-binding. This domain is
found in fungi, plants, archaea and bacteria.
Length = 104
Score = 26.6 bits (60), Expect = 3.8
Identities = 20/83 (24%), Positives = 35/83 (42%), Gaps = 18/83 (21%)
Query: 59 KKVLIVGGGDGGVAREVLKHPSVESAYLVEIDNRVIEVSKKYLPGMAVGLSDPRLTVHVG 118
K+VL+VGGG+ VA ++ L+E +V VS + L ++ + +
Sbjct: 8 KRVLVVGGGE--VALRKIRA-------LLEAGAKVTVVSPEILE------AEGLVRLIQR 52
Query: 119 DGFRFMSEHQQEFDVIITDSSDP 141
F D++I + DP
Sbjct: 53 ---EFEPGDLDGADLVIAATDDP 72
>gnl|CDD|152817 pfam12382, Peptidase_A2E, Retrotransposon peptidase. This is a
small family of fungal retroviral aspartyl peptidases.
Length = 137
Score = 27.4 bits (60), Expect = 3.8
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 14 YPSSSNRKEFGTALILDGIIQCTEF---DEFSYSEMIAFLPL 52
YP+ NRK + L+GI TEF +FS+ I+F L
Sbjct: 86 YPNKINRKTIKLIINLNGISIKTEFLVVKKFSHPAAISFTTL 127
>gnl|CDD|211312 cd06921, ChtBD1_GH19_hevein, Hevein or Type 1 chitin binding domain
subfamily co-occuring with family 19 glycosyl hydrolases
or with barwin domains. This subfamily includes Hevein,
a major IgE-binding allergen in natural rubber latex.
ChtBD1 is a lectin domain found in proteins from plants
and fungi that bind N-acetylglucosamine, plant
endochitinases, wound-induced proteins, and the alpha
subunit of Kluyveromyces lactis killer toxin. This
domain is involved in the recognition and/or binding of
chitin subunits; it typically occurs N-terminal to
glycosyl hydrolase domains in chitinases, together with
other carbohydrate-binding domains, or by itself in
tandem-repeat arrangements.
Length = 40
Score = 25.1 bits (55), Expect = 3.9
Identities = 14/29 (48%), Positives = 17/29 (58%), Gaps = 7/29 (24%)
Query: 160 ALRPGGIVCSQAGTLWYSLDCVGNTLQHC 188
AL PGG+ CSQ G W C G+T +C
Sbjct: 10 ALCPGGLCCSQWG--W----C-GSTDDYC 31
>gnl|CDD|225826 COG3288, PntA, NAD/NADP transhydrogenase alpha subunit [Energy
production and conversion].
Length = 356
Score = 27.7 bits (62), Expect = 3.9
Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 4/45 (8%)
Query: 123 FMSEHQQEFDVIITDSSDPVGPAESLFQASYFELMSRALRPGGIV 167
++E +E D++IT + P PA L A M +++PG ++
Sbjct: 237 LVAEQAKEVDIVITTALIPGRPAPKLVTAE----MVASMKPGSVI 277
>gnl|CDD|129652 TIGR00561, pntA, NAD(P) transhydrogenase, alpha subunit. This
integral membrane protein is the alpha subunit of alpha
2 beta 2 tetramer that couples the proton transport
across the membrane to the reversible transfer of
hydride ion equivalents between NAD and NADP. An
alternate name is pyridine nucleotide transhydrogenase
alpha subunit. The N-terminal region is homologous to
alanine dehydrogenase. In some species, such as
Rhodospirillum rubrum, the alpha chain is replaced by
two shorter chains, both with some homology to the
full-length alpha chain modeled here. These score below
the trusted cutoff [Energy metabolism, Electron
transport].
Length = 511
Score = 27.6 bits (61), Expect = 4.4
Identities = 32/127 (25%), Positives = 50/127 (39%), Gaps = 19/127 (14%)
Query: 58 PKKVLIVGGGDGGVAREVLKHPSVESAYLVEIDNRVIEVSKKYLPGMAVGLSDPRLTVHV 117
P KVL++G G G+A + + A + D R + G D +
Sbjct: 164 PAKVLVIGAGVAGLA--AIGAANSLGAIVRAFDTRPEVKEQVQSMGAEFLELDFKEEGGS 221
Query: 118 GDGF-RFMSE------------HQQEFDVIITDSSDPVGPAESLFQASYFELMSRALRPG 164
GDG+ + MSE +E D+IIT + P PA L E M +++ G
Sbjct: 222 GDGYAKVMSEEFIAAEMELFAAQAKEVDIIITTALIPGKPAPKLIT----EEMVDSMKAG 277
Query: 165 GIVCSQA 171
++ A
Sbjct: 278 SVIVDLA 284
>gnl|CDD|130536 TIGR01470, cysG_Nterm, siroheme synthase, N-terminal domain. This
model represents a subfamily of CysG N-terminal
region-related sequences. All sequences in the seed
alignment for this model are N-terminal regions of known
or predicted siroheme synthases. The C-terminal region
of each is uroporphyrin-III C-methyltransferase (EC
2.1.1.107), which catalyzes the first step committed to
the biosynthesis of either siroheme or cobalamin
(vitamin B12) rather than protoheme (heme). The region
represented by this model completes the process of
oxidation and iron insertion to yield siroheme. Siroheme
is a cofactor for nitrite and sulfite reductases, so
siroheme synthase is CysG of cysteine biosynthesis in
some organisms [Biosynthesis of cofactors, prosthetic
groups, and carriers, Heme, porphyrin, and cobalamin].
Length = 205
Score = 27.4 bits (61), Expect = 4.5
Identities = 15/92 (16%), Positives = 39/92 (42%), Gaps = 12/92 (13%)
Query: 50 LPLCSHPNPKKVLIVGGGDGGVAREVLKHPSVESAYLVEIDNRVIEVSKKYLPGMAVGLS 109
LP+ ++ + VL+VGGGD + + L L++ ++ ++++ + +
Sbjct: 1 LPVFANLEGRAVLVVGGGDVALRKARL---------LLKAGAQLRVIAEELESELTLLAE 51
Query: 110 DPRLTVHVGDGFRFMSEHQQEFDVIITDSSDP 141
+T F ++ + ++I + D
Sbjct: 52 QGGITWLARC---FDADILEGAFLVIAATDDE 80
>gnl|CDD|215329 PLN02610, PLN02610, probable methionyl-tRNA synthetase.
Length = 801
Score = 27.8 bits (62), Expect = 4.9
Identities = 14/46 (30%), Positives = 18/46 (39%), Gaps = 15/46 (32%)
Query: 70 GVAREVLKHPSVESAYLVEIDNRVIEVSKKYLPGMAVGLSDPRLTV 115
G+ + KHP +S Y+ EID VG PR V
Sbjct: 648 GLIVKAEKHPDADSLYVEEID---------------VGEGAPRTVV 678
>gnl|CDD|176205 cd08243, quinone_oxidoreductase_like_1, Quinone oxidoreductase
(QOR). NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The medium chain alcohol
dehydrogenase family (MDR) have a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 320
Score = 27.2 bits (61), Expect = 5.3
Identities = 18/52 (34%), Positives = 22/52 (42%), Gaps = 18/52 (34%)
Query: 126 EHQQEFDVIITDSSDPVGPA---ESLFQASYFELMSRALRPGGIVCSQAGTL 174
FD ++ + VG A +SL R LRPGGIVC G L
Sbjct: 204 AAPGGFDKVL----ELVGTATLKDSL----------RHLRPGGIVC-MTGLL 240
>gnl|CDD|234305 TIGR03672, rpl4p_arch, 50S ribosomal protein L4P. One of the
primary rRNA binding proteins, this protein initially
binds near the 5'-end of the 23S rRNA. It is important
during the early stages of 50S assembly. It makes
multiple contacts with different domains of the 23S rRNA
in the assembled 50S subunit and ribosome.
Length = 251
Score = 27.2 bits (61), Expect = 5.9
Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 10/58 (17%)
Query: 58 PKKVLIVGGGDGGVAREVLKHPSVESAYLVEIDNRVIEVSKKYLPGMAVGLSDPRLTV 115
PK VLIV G D G+++ P V+ +V ++N +E PG G RLTV
Sbjct: 192 PKSVLIVVGDDSGISKAARNLPGVD---VVTVNNLNVE---HLAPGGHPG----RLTV 239
>gnl|CDD|224288 COG1369, POP5, RNase P/RNase MRP subunit POP5 [Translation,
ribosomal structure and biogenesis].
Length = 124
Score = 26.2 bits (58), Expect = 6.5
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 3/34 (8%)
Query: 31 GIIQCTEFDEFSYSEMIAFLPLCSHPNPKKVLIV 64
GI++C + A L L N K+V+IV
Sbjct: 68 GIVRC---RREYVDLVRAALMLAREVNGKRVIIV 98
>gnl|CDD|107266 cd06271, PBP1_AglR_RafR_like, Ligand-binding domain of DNA
transcription repressors specific for raffinose (RafR)
and alpha-glucosides (AglR) which are members of the
LacI-GalR family of bacterial transcription regulators.
Ligand-binding domain of DNA transcription repressors
specific for raffinose (RafR) and alpha-glucosides
(AglR) which are members of the LacI-GalR family of
bacterial transcription regulators. The LacI-GalR family
repressors are composed of two functional domains: an
N-terminal HTH (helix-turn-helix) domain, which is
responsible for the DNA-binding specificity, and a
C-terminal ligand-binding domain, which is homologous to
the sugar-binding domain of ABC-type transport systems
that contain the type I periplasmic binding protein-like
fold. As also observed in the periplasmic binding
proteins, the C-terminal domain of the bacterial
transcription repressor undergoes a conformational
change upon ligand binding which in turn changes the DNA
binding affinity of the repressor.
Length = 268
Score = 27.2 bits (61), Expect = 6.6
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 119 DGF-RFMSEHQQEFDVIITDSSDPVGPAESLFQASYFELMSRALRPGGIVCS 169
G+ R ++E D + S D E + A+ EL++ RP IVCS
Sbjct: 140 AGYRRALAEAGLPLDPALIVSGDM--TEEGGYAAA-AELLALPDRPTAIVCS 188
>gnl|CDD|236541 PRK09496, trkA, potassium transporter peripheral membrane
component; Reviewed.
Length = 453
Score = 27.0 bits (61), Expect = 6.6
Identities = 26/102 (25%), Positives = 39/102 (38%), Gaps = 22/102 (21%)
Query: 44 SEMIAFLPLCSHPNP--KKVLIVGGGDGG--VAREVLKHPSVESAYLVEID-NRVIEVSK 98
+ A + K+V+IVGGG+ G +A+ L+ S L+E D R E+++
Sbjct: 215 EHIRAVMSEFGRLEKPVKRVMIVGGGNIGYYLAKL-LEKEGY-SVKLIERDPERAEELAE 272
Query: 99 KYLPGMAVGLSDPRLTVHVGDG----FRFMSEHQQEFDVIIT 136
+ P V GDG E E D I
Sbjct: 273 EL----------PNTLVLHGDGTDQEL-LEEEGIDEADAFIA 303
>gnl|CDD|234903 PRK01115, PRK01115, DNA polymerase sliding clamp; Validated.
Length = 247
Score = 26.7 bits (60), Expect = 6.9
Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 6/55 (10%)
Query: 119 DGFRFMSEHQQEFDVIITDSSDPV------GPAESLFQASYFELMSRALRPGGIV 167
D F +E + E +V ++ S P+ PA+S + Y + M +A V
Sbjct: 162 DKFYIEAEGEGEDEVELSLDSGPLIELSVEEPAKSSYSLDYLKDMVKATSASDEV 216
>gnl|CDD|238963 cd02005, TPP_PDC_IPDC, Thiamine pyrophosphate (TPP) family,
PDC_IPDC subfamily, TPP-binding module; composed of
proteins similar to pyruvate decarboxylase (PDC) and
indolepyruvate decarboxylase (IPDC). PDC, a key enzyme
in alcoholic fermentation, catalyzes the conversion of
pyruvate to acetaldehyde and CO2. It is able to utilize
other 2-oxo acids as substrates. In plants and various
plant-associated bacteria, IPDC plays a role in the
indole-3-pyruvic acid (IPA) pathway, a
tryptophan-dependent biosynthetic route to
indole-3-acetaldehyde (IAA). IPDC catalyzes the
decarboxylation of IPA to IAA. Both PDC and IPDC depend
on TPP and Mg2+ as cofactors.
Length = 183
Score = 26.7 bits (60), Expect = 7.1
Identities = 8/29 (27%), Positives = 16/29 (55%)
Query: 150 QASYFELMSRALRPGGIVCSQAGTLWYSL 178
QA ++ + L+P I+ ++ GT W+
Sbjct: 4 QARLWQQVQNFLKPNDILVAETGTSWFGA 32
>gnl|CDD|223996 COG1070, XylB, Sugar (pentulose and hexulose) kinases [Carbohydrate
transport and metabolism].
Length = 502
Score = 27.0 bits (60), Expect = 7.2
Identities = 12/53 (22%), Positives = 21/53 (39%), Gaps = 8/53 (15%)
Query: 15 PSSSNRKEFGTALILDGIIQCTEFDEFSYSEMIAFLPLCSHPNPKKVLIVGGG 67
R A +L+G+ F+ ++ + L P +V +VGGG
Sbjct: 367 TLPHTRAHLARA-VLEGVA-------FALADGLEALEELGGKPPSRVRVVGGG 411
>gnl|CDD|197274 cd09177, PLDc_RE_NgoFVII, Putative catalytic domain of type II
restriction enzyme NgoFVII and similar proteins.
Putative catalytic domain of type II restriction enzyme
NgoFVII (EC 3.1.21.4), which shows high sequence
similarity to type IIs restriction endonuclease BfiI.
Type II restriction endonucleases are components of
restriction modification (RM) systems that protect
bacteria and archaea against invading foreign DNA. They
usually function as homodimers or homotetramers that
cleave DNA at defined sites of 4 to 8 bp in length, and
they require Mg2+, not ATP or GTP, for catalysis. The
prototype of this subfamily is the NgoFVII restriction
endonuclease from Neisseria gonorrhoeae. It plays an
essential role in the endonucleolytic cleavage of DNA to
give specific double-stranded fragments with terminal
5'-phosphates. It recognizes the double-stranded
sequence GCSGC and cleaves after G-4. Members of this
subfamily contain one copy of the conserved HKD motif
(H-x-K-x(4)-D, where x represents any amino acid
residue) per protein chain and have been classified into
the phospholipase D (PLD, EC 3.1.4.4) superfamily.
Length = 143
Score = 26.2 bits (58), Expect = 7.4
Identities = 7/29 (24%), Positives = 17/29 (58%)
Query: 13 FYPSSSNRKEFGTALILDGIIQCTEFDEF 41
+ ++S R+++ T++IL+ I + E
Sbjct: 111 IWLTASTRRQYETSVILEDISEPAEIQLH 139
>gnl|CDD|184103 PRK13512, PRK13512, coenzyme A disulfide reductase; Provisional.
Length = 438
Score = 27.1 bits (60), Expect = 7.7
Identities = 23/96 (23%), Positives = 36/96 (37%), Gaps = 23/96 (23%)
Query: 57 NPKKVLIVGGGDGGVAREVLKHPSVESAYLVEIDNRVIEVSKKYLPGMAVGLSDP----- 111
K L+VG G ++ EVL E+ Y + +I S K M ++ P
Sbjct: 147 QVDKALVVGAG--YISLEVL-----ENLYERGLHPTLIHRSDKINKLMDADMNQPILDEL 199
Query: 112 -------RLTVHV----GDGFRFMSEHQQEFDVIIT 136
RL + G+ F S + +D+II
Sbjct: 200 DKREIPYRLNEEIDAINGNEVTFKSGKVEHYDMIIE 235
>gnl|CDD|187657 cd08954, KR_1_FAS_SDR_x, beta-ketoacyl reductase (KR) domain of
fatty acid synthase (FAS), subgroup 1, complex (x) SDRs.
NADP-dependent KR domain of the multidomain type I FAS,
a complex SDR family. This subfamily also includes
proteins identified as polyketide synthase (PKS), a
protein with related modular protein architecture and
similar function. It includes the KR domains of
mammalian and chicken FAS, and Dictyostelium discoideum
putative polyketide synthases (PKSs). These KR domains
contain two subdomains, each of which is related to SDR
Rossmann fold domains. However, while the C-terminal
subdomain has an active site similar to the other SDRs
and a NADP-binding capability, the N-terminal SDR-like
subdomain is truncated and lacks these functions,
serving a supportive structural role. In some instances,
such as porcine FAS, an enoyl reductase (a Rossman fold
NAD-binding domain of the medium-chain
dehydrogenase/reductase, MDR family) module is inserted
between the sub-domains. Fatty acid synthesis occurs via
the stepwise elongation of a chain (which is attached to
acyl carrier protein, ACP) with 2-carbon units.
Eukaryotic systems consists of large, multifunctional
synthases (type I) while bacterial, type II systems, use
single function proteins. Fungal fatty acid synthesis
uses a dodecamer of 6 alpha and 6 beta subunits. In
mammalian type FAS cycles, ketoacyl synthase forms
acetoacetyl-ACP which is reduced by the NADP-dependent
beta-ketoacyl reductase (KR), forming
beta-hydroxyacyl-ACP, which is in turn dehydrated by
dehydratase to a beta-enoyl intermediate, which is
reduced by NADP-dependent beta-enoyl reductase (ER);
this KR and ER are members of the SDR family. This KR
subfamily has an active site tetrad with a similar 3D
orientation compared to archetypical SDRs, but the
active site Lys and Asn residue positions are swapped.
The characteristic NADP-binding is typical of the
multidomain complex SDRs, with a GGXGXXG NADP binding
motif. 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
prostaglandin dehydrogenase (PGDH) numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107,
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 KRs 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 = 452
Score = 26.6 bits (59), Expect = 8.6
Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 12/57 (21%)
Query: 55 HPNPKKVLIVGGGDGGVAREVLKHPSVESAYLVEIDNR--VIEVSKKYLPGMAVGLS 109
N K ++ GG GG+ E+LK LV+ +I +S+ GM L
Sbjct: 214 PINLGKSYLITGGSGGLGLEILKW-------LVKRGAVENIIILSRS---GMKWELE 260
>gnl|CDD|234119 TIGR03140, AhpF, alkyl hydroperoxide reductase subunit F. This
enzyme is the partner of the peroxiredoxin (alkyl
hydroperoxide reductase) AhpC which contains the
peroxide-reactive cysteine. AhpF contains the reductant
(NAD(P)H) binding domain (pfam00070) and presumably acts
to resolve the disulfide which forms after oxidation of
the active site cysteine in AphC. This proteins contains
two paired conserved cysteine motifs, CxxCP and CxHCDGP
[Cellular processes, Detoxification, Cellular processes,
Adaptations to atypical conditions].
Length = 515
Score = 26.6 bits (59), Expect = 9.7
Identities = 10/27 (37%), Positives = 16/27 (59%), Gaps = 2/27 (7%)
Query: 47 IAFLPLCSHP--NPKKVLIVGGGDGGV 71
+A+ P C P K V ++GGG+ G+
Sbjct: 339 VAYCPHCDGPFFKGKDVAVIGGGNSGI 365
>gnl|CDD|222236 pfam13578, Methyltransf_24, Methyltransferase domain. This family
appears to be a methyltransferase domain.
Length = 105
Score = 25.7 bits (57), Expect = 9.8
Identities = 14/59 (23%), Positives = 22/59 (37%), Gaps = 6/59 (10%)
Query: 110 DPRLTVHVGDGFRFMSEHQQE-FDVIITDSSDPVGPAESLFQASYFELMSRALRPGGIV 167
R+ + GD ++ D++ D D A + EL L PGGI+
Sbjct: 47 ADRVRLLRGDSLEALARLPDGSIDLLFIDG-DHTYEA----VLADLELWLPLLAPGGII 100
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 0.419
Gapped
Lambda K H
0.267 0.0829 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,129,306
Number of extensions: 948852
Number of successful extensions: 1139
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1118
Number of HSP's successfully gapped: 79
Length of query: 197
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 105
Effective length of database: 6,857,034
Effective search space: 719988570
Effective search space used: 719988570
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: 56 (25.2 bits)