RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16850
(174 letters)
>gnl|CDD|233587 TIGR01821, 5aminolev_synth, 5-aminolevulinic acid synthase. This
model represents 5-aminolevulinic acid synthase, an
enzyme for one of two routes to the heme precursor
5-aminolevulinate. The protein is a pyridoxal
phosphate-dependent enzyme related to
2-amino-3-ketobutyrate CoA tranferase and
8-amino-7-oxononanoate synthase. This enzyme appears
restricted to the alpha Proteobacteria and mitochondrial
derivatives [Biosynthesis of cofactors, prosthetic
groups, and carriers, Heme, porphyrin, and cobalamin].
Length = 402
Score = 188 bits (479), Expect = 5e-59
Identities = 70/130 (53%), Positives = 91/130 (70%), Gaps = 1/130 (0%)
Query: 9 FPYEDFFHEQIMKKKRDHSYRVFKKVNRLATNFP-AAYEYTDSEKEVTVYCSNDYLGMSC 67
Y+ FF+++I K + YRVF + R A FP A + D K+VTV+CSNDYLGM
Sbjct: 1 MDYDQFFNKEIDKLHLEGRYRVFADLERQAGEFPFAQWHRPDGAKDVTVWCSNDYLGMGQ 60
Query: 68 HPKVKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQKEAGLVFTSCYVANDS 127
HP+V A+ E L+K+G GAGGTRNISG ++ H +LE ++A LH KE+ LVFTS YVAND+
Sbjct: 61 HPEVLQAMHETLDKYGAGAGGTRNISGTNIPHVELEAELADLHGKESALVFTSGYVANDA 120
Query: 128 TLFTLGKMIP 137
TL TL K+IP
Sbjct: 121 TLATLAKIIP 130
>gnl|CDD|236370 PRK09064, PRK09064, 5-aminolevulinate synthase; Validated.
Length = 407
Score = 178 bits (453), Expect = 6e-55
Identities = 71/130 (54%), Positives = 89/130 (68%), Gaps = 2/130 (1%)
Query: 10 PYEDFFHEQIMKKKRDHSYRVFKKVNRLATNFPAAYEYTD--SEKEVTVYCSNDYLGMSC 67
YE FF + + K + YRVF + R+A FP A E+EVTV+CSNDYLGM
Sbjct: 2 DYEAFFENALDRLKAEGRYRVFADLERIAGRFPYATWRRPDGGEREVTVWCSNDYLGMGQ 61
Query: 68 HPKVKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQKEAGLVFTSCYVANDS 127
HPKV A+ EAL++ G GAGGTRNISG + +H +LE ++A LH KEA LVFTS YV+ND+
Sbjct: 62 HPKVIEAMIEALDRCGAGAGGTRNISGTNHYHVELERELADLHGKEAALVFTSGYVSNDA 121
Query: 128 TLFTLGKMIP 137
TL TL K+IP
Sbjct: 122 TLSTLAKLIP 131
>gnl|CDD|184024 PRK13393, PRK13393, 5-aminolevulinate synthase; Provisional.
Length = 406
Score = 166 bits (422), Expect = 2e-50
Identities = 66/130 (50%), Positives = 85/130 (65%), Gaps = 1/130 (0%)
Query: 9 FPYEDFFHEQIMKKKRDHSYRVFKKVNRLATNFP-AAYEYTDSEKEVTVYCSNDYLGMSC 67
YE +F Q+ +R+ YRVF + R A FP A + D +EVTV+CSNDYLGM
Sbjct: 1 MNYEQYFQRQLDGLRREGRYRVFADLERQAGAFPRATHHGPDGPREVTVWCSNDYLGMGQ 60
Query: 68 HPKVKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQKEAGLVFTSCYVANDS 127
HP V +A+ EAL+ G GAGGTRNISG + +H LE ++A LH KEA L+FTS YV+N +
Sbjct: 61 HPAVLAAMHEALDTCGAGAGGTRNISGTNHYHVLLEAELADLHGKEAALLFTSGYVSNWA 120
Query: 128 TLFTLGKMIP 137
L TLG +P
Sbjct: 121 ALSTLGSRLP 130
>gnl|CDD|184023 PRK13392, PRK13392, 5-aminolevulinate synthase; Provisional.
Length = 410
Score = 153 bits (387), Expect = 3e-45
Identities = 62/130 (47%), Positives = 85/130 (65%), Gaps = 1/130 (0%)
Query: 9 FPYEDFFHEQIMKKKRDHSYRVFKKVNRLATNFPAA-YEYTDSEKEVTVYCSNDYLGMSC 67
Y+ +F + + ++ YRVF + R A FP A D + VT++CSNDYLGM
Sbjct: 2 MNYDSYFDAALAQLHQEGRYRVFADLEREAGRFPRARDHGPDGPRRVTIWCSNDYLGMGQ 61
Query: 68 HPKVKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQKEAGLVFTSCYVANDS 127
HP V A+ +AL+++G GAGGTRNISG S H LE ++A LH KE+ L+FTS YV+ND+
Sbjct: 62 HPDVIGAMVDALDRYGAGAGGTRNISGTSHPHVLLERELADLHGKESALLFTSGYVSNDA 121
Query: 128 TLFTLGKMIP 137
L TLGK++P
Sbjct: 122 ALSTLGKLLP 131
>gnl|CDD|99747 cd06454, KBL_like, KBL_like; this family belongs to the pyridoxal
phosphate (PLP)-dependent aspartate aminotransferase
superfamily (fold I). The major groups in this CD
corresponds to serine palmitoyltransferase (SPT),
5-aminolevulinate synthase (ALAS),
8-amino-7-oxononanoate synthase (AONS), and
2-amino-3-ketobutyrate CoA ligase (KBL). SPT is
responsible for the condensation of L-serine with
palmitoyl-CoA to produce 3-ketodihydrospingosine, the
reaction of the first step in sphingolipid biosynthesis.
ALAS is involved in heme biosynthesis; it catalyzes the
synthesis of 5-aminolevulinic acid from glycine and
succinyl-coenzyme A. AONS catalyses the decarboxylative
condensation of l-alanine and pimeloyl-CoA in the first
committed step of biotin biosynthesis. KBL catalyzes the
second reaction step of the metabolic degradation
pathway for threonine converting 2-amino-3-ketobutyrate,
to glycine and acetyl-CoA. The members of this CD are
widely found in all three forms of life.
Length = 349
Score = 134 bits (341), Expect = 6e-39
Identities = 48/83 (57%), Positives = 61/83 (73%)
Query: 52 KEVTVYCSNDYLGMSCHPKVKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQ 111
K+V +CSNDYLG++ HP+V A +EAL+K+G GAGG+R ISG S HE+LEE++A H
Sbjct: 1 KKVLNFCSNDYLGLANHPEVIEAAKEALDKYGVGAGGSRLISGTSDLHEELEEELAEFHG 60
Query: 112 KEAGLVFTSCYVANDSTLFTLGK 134
KEA LVF+S Y AND L TL
Sbjct: 61 KEAALVFSSGYAANDGVLSTLAG 83
>gnl|CDD|223234 COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related
enzymes [Coenzyme metabolism].
Length = 388
Score = 131 bits (332), Expect = 3e-37
Identities = 43/124 (34%), Positives = 68/124 (54%), Gaps = 5/124 (4%)
Query: 11 YEDFFHEQIMKKKRDHSYRVFKKVNRLATNFPAAYEYTDSEKEVTVYCSNDYLGMSCHPK 70
+ F + + K + YR + ++R ++V +CSNDYLG++ HP+
Sbjct: 3 FLSFLRQALQALKAEGLYRGLRALDR-----RQGLAIRADGRKVLNFCSNDYLGLASHPE 57
Query: 71 VKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQKEAGLVFTSCYVANDSTLF 130
+ A + A+ ++G GAGG+R ISG S H +LEE++A EA L+F+S +VAN L
Sbjct: 58 LIEAAKAAIRRYGVGAGGSRLISGTSDLHVELEEELADFLGAEAALLFSSGFVANLGLLS 117
Query: 131 TLGK 134
L K
Sbjct: 118 ALLK 121
>gnl|CDD|129937 TIGR00858, bioF, 8-amino-7-oxononanoate synthase.
7-keto-8-aminopelargonic acid synthetase is an alternate
name. This model represents 8-amino-7-oxononanoate
synthase, the BioF protein of biotin biosynthesis. This
model is based on a careful phylogenetic analysis to
separate members of this family from
2-amino-3-ketobutyrate and other related pyridoxal
phosphate-dependent enzymes. In several species,
including Staphylococcus and Coxiella, a candidate
8-amino-7-oxononanoate synthase is confirmed by location
in the midst of a biotin biosynthesis operon but scores
below the trusted cutoff of this model [Biosynthesis of
cofactors, prosthetic groups, and carriers, Biotin].
Length = 360
Score = 101 bits (253), Expect = 6e-26
Identities = 33/82 (40%), Positives = 53/82 (64%)
Query: 51 EKEVTVYCSNDYLGMSCHPKVKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLH 110
+ + + SNDYLG++ HP+V A ++ E++G G+ +R +SGNS HE+LEE++A
Sbjct: 15 GRRLLNFSSNDYLGLASHPEVIQAAQQGAEQYGAGSTASRLVSGNSPLHEELEEELAEWK 74
Query: 111 QKEAGLVFTSCYVANDSTLFTL 132
EA L+F+S Y+AN + L
Sbjct: 75 GTEAALLFSSGYLANVGVISAL 96
>gnl|CDD|235655 PRK05958, PRK05958, 8-amino-7-oxononanoate synthase; Reviewed.
Length = 385
Score = 96.8 bits (242), Expect = 3e-24
Identities = 37/110 (33%), Positives = 60/110 (54%), Gaps = 5/110 (4%)
Query: 23 KRDHSYRVFKKVNRLATNFPAAYEYTDSEKEVTVYCSNDYLGMSCHPKVKSAVREALEKF 82
+ YR R + D + + + SNDYLG++ HP++ +A ++A ++
Sbjct: 15 RAAGLYRSL----RPREGGAGRWLVVDGRRMLN-FASNDYLGLARHPRLIAAAQQAARRY 69
Query: 83 GTGAGGTRNISGNSLFHEKLEEDVARLHQKEAGLVFTSCYVANDSTLFTL 132
G G+GG+R ++GNS HE LEE++A E L+F+S Y AN + L L
Sbjct: 70 GAGSGGSRLVTGNSPAHEALEEELAEWFGAERALLFSSGYAANLAVLTAL 119
>gnl|CDD|130884 TIGR01825, gly_Cac_T_rel, pyridoxal phosphate-dependent
acyltransferase, putative. This model represents an
enzyme subfamily related to three known enzymes; it
appears closest to glycine C-acteyltransferase, shows no
overlap with it in species distribution, and may share
that function. The three closely related enzymes are
glycine C-acetyltransferase (2-amino-3-ketobutyrate
coenzyme A ligase), 5-aminolevulinic acid synthase, and
8-amino-7-oxononanoate synthase. All transfer the
R-group (acetyl, succinyl, or 6-carboxyhexanoyl) from
coenzyme A to an amino acid (Gly, Gly, Ala,
respectively), with release of CO2 for the latter two
reactions.
Length = 385
Score = 75.6 bits (186), Expect = 1e-16
Identities = 34/78 (43%), Positives = 49/78 (62%)
Query: 52 KEVTVYCSNDYLGMSCHPKVKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQ 111
KEV SN+YLG + HP++K A +A++++G GAG R I+G HE+LEE +A+ +
Sbjct: 33 KEVINLSSNNYLGFADHPRLKEAAAQAIQQYGVGAGAVRTIAGTLRLHEELEEKLAKFKK 92
Query: 112 KEAGLVFTSCYVANDSTL 129
EA LVF S + N L
Sbjct: 93 TEAALVFQSGFNTNQGVL 110
>gnl|CDD|235893 PRK06939, PRK06939, 2-amino-3-ketobutyrate coenzyme A ligase;
Provisional.
Length = 397
Score = 74.1 bits (183), Expect = 5e-16
Identities = 30/83 (36%), Positives = 49/83 (59%), Gaps = 3/83 (3%)
Query: 52 KEVTVYCSNDYLGMSCHPKVKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQ 111
KEV +C+N+YLG++ HP++ +A + AL+ G G R I G H++LEE +A+
Sbjct: 42 KEVINFCANNYLGLANHPELIAAAKAALDSHGFGMASVRFICGTQDLHKELEEKLAKFLG 101
Query: 112 KEAGLVFTSCYVAND---STLFT 131
E ++++SC+ AN TL
Sbjct: 102 TEDAILYSSCFDANGGLFETLLG 124
>gnl|CDD|130881 TIGR01822, 2am3keto_CoA, 2-amino-3-ketobutyrate coenzyme A ligase.
This model represents a narrowly defined clade of animal
and bacterial (almost exclusively Proteobacterial)
2-amino-3-ketobutyrate--CoA ligase. This enzyme can act
in threonine catabolism. The closest homolog from
Bacillus subtilis, and sequences like it, may be
functionally equivalent but were not included in the
model because of difficulty in finding reports of
function [Energy metabolism, Amino acids and amines].
Length = 393
Score = 69.4 bits (170), Expect = 2e-14
Identities = 27/74 (36%), Positives = 44/74 (59%)
Query: 52 KEVTVYCSNDYLGMSCHPKVKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQ 111
+EV +C+N+YLG+S HP + A ++AL++ G G R I G H++LE +A
Sbjct: 38 REVLNFCANNYLGLSSHPDLIQAAKDALDEHGFGMSSVRFICGTQDIHKELEAKIAAFLG 97
Query: 112 KEAGLVFTSCYVAN 125
E +++ SC+ AN
Sbjct: 98 TEDTILYASCFDAN 111
>gnl|CDD|178541 PLN02955, PLN02955, 8-amino-7-oxononanoate synthase.
Length = 476
Score = 59.3 bits (143), Expect = 6e-11
Identities = 28/84 (33%), Positives = 49/84 (58%)
Query: 52 KEVTVYCSNDYLGMSCHPKVKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQ 111
K++ ++ NDYLG+S HP + +A A +++G G G+ I G + +H LE +A L +
Sbjct: 102 KKLLLFSGNDYLGLSSHPTISNAAANAAKEYGMGPKGSALICGYTTYHRLLESSLADLKK 161
Query: 112 KEAGLVFTSCYVANDSTLFTLGKM 135
KE LV + + AN + + +G +
Sbjct: 162 KEDCLVCPTGFAANMAAMVAIGSV 185
>gnl|CDD|215756 pfam00155, Aminotran_1_2, Aminotransferase class I and II.
Length = 357
Score = 51.2 bits (123), Expect = 4e-08
Identities = 26/94 (27%), Positives = 41/94 (43%), Gaps = 13/94 (13%)
Query: 52 KEVTVYCSNDYLGMSCHPKVKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLH- 110
+ SN+YLG S + + + + AGGTRN+ G + +L E +A+
Sbjct: 1 TDKINLGSNEYLGDS--GTLPAVAKAEKD---ALAGGTRNLYGPTDGLPELREALAKFLG 55
Query: 111 -------QKEAGLVFTSCYVANDSTLFTLGKMIP 137
+EA +VF S AN L L ++ P
Sbjct: 56 RSPVLKLDREAAVVFGSGAGANIEALIFLLRLNP 89
>gnl|CDD|178101 PLN02483, PLN02483, serine palmitoyltransferase.
Length = 489
Score = 47.8 bits (114), Expect = 6e-07
Identities = 26/79 (32%), Positives = 38/79 (48%), Gaps = 9/79 (11%)
Query: 59 SNDYLGMS-----CHPKVKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQKE 113
S +YLG + C P+V E+L+K+ +R G + H +LEE VAR K
Sbjct: 107 SYNYLGFAAADEYCTPRVI----ESLKKYSASTCSSRVDGGTTKLHRELEELVARFVGKP 162
Query: 114 AGLVFTSCYVANDSTLFTL 132
A +VF Y N + + L
Sbjct: 163 AAIVFGMGYATNSTIIPAL 181
>gnl|CDD|178417 PLN02822, PLN02822, serine palmitoyltransferase.
Length = 481
Score = 45.9 bits (109), Expect = 3e-06
Identities = 27/88 (30%), Positives = 43/88 (48%), Gaps = 7/88 (7%)
Query: 52 KEVTVYCSNDYLGMSCHPKVKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQ 111
K+V + S +YLG+ + K+K + ALEK+G G+ G R G H E +A+
Sbjct: 109 KDVVNFASANYLGLIGNEKIKESCTSALEKYGVGSCGPRGFYGTIDVHLDCETKIAKFLG 168
Query: 112 KEAGLVFTSCYVANDSTLFTLGKMIPYF 139
++ Y ST+F++ IP F
Sbjct: 169 TPDSIL----YSYGLSTIFSV---IPAF 189
>gnl|CDD|102071 PRK05937, PRK05937, 8-amino-7-oxononanoate synthase; Provisional.
Length = 370
Score = 45.2 bits (107), Expect = 4e-06
Identities = 23/76 (30%), Positives = 33/76 (43%), Gaps = 7/76 (9%)
Query: 57 YCSNDYLGMSCHPKVKSAV----REALEKFG---TGAGGTRNISGNSLFHEKLEEDVARL 109
+ +ND+LG S + V R +F G GG+R I G S + LE +A
Sbjct: 9 FVTNDFLGFSRSDTLVHEVEKRYRLYCRQFPHAQLGYGGSRAILGPSSLLDDLEHKIAHF 68
Query: 110 HQKEAGLVFTSCYVAN 125
H + S Y+AN
Sbjct: 69 HGAPEAFIVPSGYMAN 84
>gnl|CDD|178766 PLN03227, PLN03227, serine palmitoyltransferase-like protein;
Provisional.
Length = 392
Score = 42.6 bits (100), Expect = 3e-05
Identities = 19/79 (24%), Positives = 37/79 (46%)
Query: 56 VYCSNDYLGMSCHPKVKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQKEAG 115
+ ++D+L S P ++ E+L +G G+ G R G H +LE+ +A E+
Sbjct: 2 NFATHDFLSTSSSPTLRQTALESLSHYGCGSCGPRGFYGTIDAHLELEQCMAEFLGTESA 61
Query: 116 LVFTSCYVANDSTLFTLGK 134
++++ ST+ K
Sbjct: 62 ILYSDGASTTSSTVAAFAK 80
>gnl|CDD|181006 PRK07505, PRK07505, hypothetical protein; Provisional.
Length = 402
Score = 41.5 bits (98), Expect = 9e-05
Identities = 27/121 (22%), Positives = 39/121 (32%), Gaps = 18/121 (14%)
Query: 26 HSYRVFKKVNRLA------------TNFPAA-----YEYTDSEKEVTVYCSNDYLGMSCH 68
H YR KK A + S YLG+ H
Sbjct: 3 HKYRNNKKRINRAEKFWDAAYDEGLNGLTVGEREGILITLADGHTFVNFVSCSYLGLDTH 62
Query: 69 PKVKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQKEAGLVFTSCYVANDST 128
P + +AL++ G+ + S + LEE ++ L L FTSC A+
Sbjct: 63 PAIIEGAVDALKRTGSLHLSSSRTRVRSQILKDLEEALSELFGASV-LTFTSCSAAHLGI 121
Query: 129 L 129
L
Sbjct: 122 L 122
>gnl|CDD|180866 PRK07179, PRK07179, hypothetical protein; Provisional.
Length = 407
Score = 35.4 bits (82), Expect = 0.010
Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 10/72 (13%)
Query: 59 SNDYLGMSCHPKVKSAVREALEKFGTGAGGTRNISGNSLFHE-----KLEEDVARLHQKE 113
SNDYL +S HP + A AL++ G + H+ + E+ +A E
Sbjct: 61 SNDYLNLSGHPDIIKAQIAALQEEGDSL-----VMSAVFLHDDSPKPQFEKKLAAFTGFE 115
Query: 114 AGLVFTSCYVAN 125
+ L+ S + AN
Sbjct: 116 SCLLCQSGWAAN 127
>gnl|CDD|236149 PRK08088, PRK08088, 4-aminobutyrate aminotransferase; Validated.
Length = 425
Score = 33.2 bits (76), Expect = 0.053
Identities = 29/102 (28%), Positives = 40/102 (39%), Gaps = 36/102 (35%)
Query: 68 HPKVKSAVREALEKF-------------------------GTGAGGTRNISGNSLFHEKL 102
HPKV +AV L+K G A T ++ S E +
Sbjct: 59 HPKVVAAVEAQLKKLSHTCFQVLAYEPYLELCEKMNQKVPGDFAKKTLLVTTGS---EAV 115
Query: 103 EEDV--ARLHQKEAGLV-FTSCYVANDSTLFTL---GKMIPY 138
E V AR K +G++ FT Y + T +TL GK+ PY
Sbjct: 116 ENAVKIARAATKRSGVIAFTGAY--HGRTHYTLALTGKVNPY 155
>gnl|CDD|179505 PRK02936, argD, acetylornithine aminotransferase; Provisional.
Length = 377
Score = 32.2 bits (74), Expect = 0.094
Identities = 19/54 (35%), Positives = 26/54 (48%), Gaps = 11/54 (20%)
Query: 67 CHPKVKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARL--HQKEAGLVF 118
CHP V AV+E L+ ++S +LF L+E+VA L LVF
Sbjct: 46 CHPTVTKAVQEQLDDIW-------HVS--NLFTNSLQEEVASLLAENSAGDLVF 90
>gnl|CDD|234607 PRK00062, PRK00062, glutamate-1-semialdehyde aminotransferase;
Provisional.
Length = 426
Score = 30.0 bits (69), Expect = 0.55
Identities = 11/21 (52%), Positives = 12/21 (57%), Gaps = 3/21 (14%)
Query: 67 CHPKVKSAVREALEK---FGT 84
HP+V AV EA EK FG
Sbjct: 67 AHPEVVEAVIEAAEKGLSFGA 87
>gnl|CDD|132910 cd07032, RNAP_I_II_AC40, AC40 subunit of Eukaryotic RNA polymerase
(RNAP) I and RNAP III. The eukaryotic AC40 subunit of
RNA polymerase (RNAP) I and RNAP III is involved in the
assembly of RNAP subunits. RNAP is a large multi-subunit
complex responsible for the synthesis of RNA. It is the
principal enzyme of the transcription process, and is a
final target in many regulatory pathways that control
gene expression in all living cells. At least three
distinct RNAP complexes are found in eukaryotic nuclei:
RNAP I, RNAP II, and RNAP III. RNAP I is responsible for
the synthesis of ribosomal RNA precursor, while RNAP III
functions in the synthesis of 5S and tRNA. The AC40
subunit is the equivalent of the RPB3 subunit of RNAP
II. The RPB3 subunit is similar to the bacterial RNAP
alpha subunit in that it contains two subdomains: one
subdomain is similar the eukaryotic Rpb11/AC19/archaeal
L subunit which is involved in dimerization; and the
other is an inserted beta sheet subdomain. The RPB3
subunit heterodimerizes with the RPB11 subunit, and
together with RPB10 and RPB12, anchors the two largest
subunits, RPB1 and RPB2, and stabilizes their
association. The homology of AC40 to RPB3 suggests a
similar function. The AC40 subunit is likely to
associate with the RPB11 counterpart, AC19, to form a
heterodimer, which stabilizes the association of the two
largest subunits of RNAP I and RNAP III.
Length = 291
Score = 29.9 bits (68), Expect = 0.63
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 2 DTTMREPFPYEDFFHEQIMKKKRDH 26
DT RE +E+F + + + RDH
Sbjct: 233 DTLSREVLRHEEFKDKVELGRVRDH 257
>gnl|CDD|235404 PRK05319, rplD, 50S ribosomal protein L4; Provisional.
Length = 205
Score = 29.3 bits (67), Expect = 0.77
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 22 KKRDHSYRVFKKVNRLA 38
K RD+S ++ KKV RLA
Sbjct: 92 KPRDYSQKLNKKVRRLA 108
>gnl|CDD|234414 TIGR03953, rplD_bact, 50S ribosomal protein L4,
bacterial/organelle. Members of this protein family
are ribosomal protein L4. This model recognizes
bacterial and most organellar forms, but excludes
homologs from the eukaryotic cytoplasm and from archaea
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 188
Score = 29.4 bits (67), Expect = 0.78
Identities = 11/17 (64%), Positives = 14/17 (82%)
Query: 22 KKRDHSYRVFKKVNRLA 38
K RD+SY++ KKV RLA
Sbjct: 77 KPRDYSYKLNKKVRRLA 93
>gnl|CDD|235599 PRK05769, PRK05769, 4-aminobutyrate aminotransferase;
Provisional.
Length = 441
Score = 29.5 bits (67), Expect = 0.82
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 67 CHPKVKSAVREALEKFGTGAG 87
HPKV AV+E EKF +
Sbjct: 71 AHPKVVKAVKEQAEKFLHYSL 91
>gnl|CDD|236032 PRK07495, PRK07495, 4-aminobutyrate aminotransferase;
Provisional.
Length = 425
Score = 28.9 bits (65), Expect = 1.2
Identities = 7/16 (43%), Positives = 12/16 (75%)
Query: 67 CHPKVKSAVREALEKF 82
HP+V +AV+ L++F
Sbjct: 57 RHPRVIAAVKAQLDRF 72
>gnl|CDD|181234 PRK08117, PRK08117, 4-aminobutyrate aminotransferase;
Provisional.
Length = 433
Score = 29.2 bits (66), Expect = 1.2
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 67 CHPKVKSAVREALEKFGTGAGG 88
HPKV A++E +K G G
Sbjct: 60 RHPKVVQAIKEQADKLMHGPSG 81
>gnl|CDD|235807 PRK06460, PRK06460, hypothetical protein; Provisional.
Length = 376
Score = 28.6 bits (64), Expect = 1.6
Identities = 10/35 (28%), Positives = 16/35 (45%)
Query: 100 EKLEEDVARLHQKEAGLVFTSCYVANDSTLFTLGK 134
+L + + L E G+ F+S A +T L K
Sbjct: 48 LELTKKIVELENAEMGVAFSSGMGAISTTALALLK 82
>gnl|CDD|187568 cd05258, CDP_TE_SDR_e, CDP-tyvelose 2-epimerase, extended (e) SDRs.
CDP-tyvelose 2-epimerase is a tetrameric SDR that
catalyzes the conversion of CDP-D-paratose to
CDP-D-tyvelose, the last step in tyvelose biosynthesis.
This subgroup is a member of the extended SDR subfamily,
with a characteristic active site tetrad and NAD-binding
motif. Extended SDRs are distinct from classical SDRs.
In addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
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 numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, 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. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. 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.
Length = 337
Score = 28.0 bits (63), Expect = 2.7
Identities = 17/52 (32%), Positives = 21/52 (40%), Gaps = 11/52 (21%)
Query: 69 PKVKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQKEAGLVFTS 120
P V ++ F T A GT N+ LE AR H A +FTS
Sbjct: 84 PSVTTSASSPRLDFETNALGTLNV---------LE--AARQHAPNAPFIFTS 124
>gnl|CDD|226647 COG4181, COG4181, Predicted ABC-type transport system involved in
lysophospholipase L1 biosynthesis, ATPase component
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 228
Score = 27.4 bits (61), Expect = 3.6
Identities = 14/49 (28%), Positives = 20/49 (40%), Gaps = 1/49 (2%)
Query: 72 KSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQKEAGLVFTS 120
KS + L + G + G L H+ E+ A L + G VF S
Sbjct: 49 KSTLLAVLAGLDDPSSGEVRLLGQPL-HKLDEDARAALRARHVGFVFQS 96
>gnl|CDD|215203 PLN02355, PLN02355, probable galactinol--sucrose
galactosyltransferase 1.
Length = 758
Score = 27.5 bits (61), Expect = 3.8
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 5/61 (8%)
Query: 71 VKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQKEAGLVFTSCYVANDSTLF 130
VK V+ LE G G GG ++ +H+ LE +AR + G++ SC N L+
Sbjct: 391 VKVDVQNILETLGAGHGGRVKLARK--YHQALEASIARNFP-DNGII--SCMSHNTDGLY 445
Query: 131 T 131
+
Sbjct: 446 S 446
>gnl|CDD|223166 COG0088, RplD, Ribosomal protein L4 [Translation, ribosomal
structure and biogenesis].
Length = 214
Score = 27.2 bits (61), Expect = 4.3
Identities = 19/63 (30%), Positives = 27/63 (42%), Gaps = 6/63 (9%)
Query: 21 KKKRDHSYRVFKKVNRLATNFPAAYEYTDSEKEVTVYCSNDYLGMSCHPKVKSAVREALE 80
K +RD+S ++ KK RLA +A ++ V PK K V E L+
Sbjct: 93 KPERDYSQKLNKKERRLALR--SALSAKARAGKLVVV---RGHVFEDAPKTKELV-EFLK 146
Query: 81 KFG 83
K G
Sbjct: 147 KLG 149
>gnl|CDD|236414 PRK09213, PRK09213, pur operon repressor; Provisional.
Length = 271
Score = 27.1 bits (61), Expect = 4.8
Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 14/76 (18%)
Query: 75 VREALEKFGTG--------AGGTRNISGNSL--FHEKLEEDVARLHQKE----AGLVFTS 120
++E EK G G AGG + I S E +EE RL + + G ++ S
Sbjct: 47 IKETFEKQGIGTLETVPGAAGGVKYIPSISEEEAREFVEELCERLSEPDRILPGGYLYLS 106
Query: 121 CYVANDSTLFTLGKMI 136
+ N S L +G++I
Sbjct: 107 DLLGNPSILRKIGRII 122
>gnl|CDD|180690 PRK06777, PRK06777, 4-aminobutyrate aminotransferase;
Provisional.
Length = 421
Score = 27.1 bits (60), Expect = 5.7
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 68 HPKVKSAVREALEKF 82
HPKV +AVR+ L++F
Sbjct: 58 HPKVVAAVRQQLDQF 72
>gnl|CDD|225885 COG3349, COG3349, Uncharacterized conserved protein [Function
unknown].
Length = 485
Score = 27.0 bits (60), Expect = 5.8
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 43 AAYEYTDSEKEVTVYCSNDYLG 64
AAYE D+ +VT+Y + D LG
Sbjct: 15 AAYELADAGYDVTLYEARDRLG 36
>gnl|CDD|223238 COG0160, GabT, 4-aminobutyrate aminotransferase and related
aminotransferases [Amino acid transport and
metabolism].
Length = 447
Score = 26.8 bits (60), Expect = 6.2
Identities = 9/20 (45%), Positives = 11/20 (55%), Gaps = 1/20 (5%)
Query: 63 LGMSCHPKVKSAVREALEKF 82
LG HP+V AV+ L K
Sbjct: 70 LGH-NHPRVVEAVKRQLAKL 88
>gnl|CDD|181005 PRK07503, PRK07503, methionine gamma-lyase; Provisional.
Length = 403
Score = 27.1 bits (60), Expect = 6.4
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 102 LEEDVARLHQKEAGLVFTSCYVANDSTLFTL 132
LE+ +A L EA + S A +TL+TL
Sbjct: 70 LEQRMASLEGGEAAVALASGMGAITATLWTL 100
>gnl|CDD|223080 COG0001, HemL, Glutamate-1-semialdehyde aminotransferase
[Coenzyme metabolism].
Length = 432
Score = 26.8 bits (60), Expect = 6.7
Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 3/20 (15%)
Query: 68 HPKVKSAVREALEK---FGT 84
HP V AV+E LE+ FG
Sbjct: 71 HPAVVEAVQEQLERGLSFGA 90
>gnl|CDD|201078 pfam00202, Aminotran_3, Aminotransferase class-III.
Length = 338
Score = 26.9 bits (60), Expect = 6.7
Identities = 16/56 (28%), Positives = 24/56 (42%), Gaps = 10/56 (17%)
Query: 67 CHPKVKSAVREALEKFGTGAGGTRNISGNSLFHE---KLEEDVARLHQKEAGLVFT 119
CHPK+ AV+E +K + S + E +L E +A+L VF
Sbjct: 33 CHPKIVQAVKEQADKL-------THTSFRAFTTEPALQLAEKLAQLTPGGLDRVFF 81
>gnl|CDD|237144 PRK12582, PRK12582, acyl-CoA synthetase; Provisional.
Length = 624
Score = 26.9 bits (60), Expect = 6.9
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 68 HPKVKSAVREALEKFGTGAGG 88
HP V + +RE L AGG
Sbjct: 548 HPAVLAILREGLSAHNAEAGG 568
>gnl|CDD|180685 PRK06767, PRK06767, methionine gamma-lyase; Provisional.
Length = 386
Score = 26.7 bits (59), Expect = 7.9
Identities = 12/33 (36%), Positives = 14/33 (42%)
Query: 102 LEEDVARLHQKEAGLVFTSCYVANDSTLFTLGK 134
EE +A L E L F S A +TL K
Sbjct: 66 FEERMAVLEGGEEALAFGSGMAAISATLIGFLK 98
>gnl|CDD|233098 TIGR00707, argD, transaminase, acetylornithine/succinylornithine
family. This family of proteins, for which ornithine
aminotransferases form an outgroup, consists mostly of
proteins designated acetylornithine aminotransferase.
However, the two very closely related members from E.
coli are assigned different enzymatic activities. One is
acetylornithine aminotransferase (EC 2.6.1.11), ArgD, an
enzyme of arginine biosynthesis, while another is
succinylornithine aminotransferase, an enzyme of the
arginine succinyltransferase pathway, an
ammonia-generating pathway of arginine catabolism (See
MEDLINE:98361920). Members of this family may also act
on ornithine, like ornithine aminotransferase (EC
2.6.1.13) (see MEDLINE:90337349) and on
succinyldiaminopimelate, like
N-succinyldiaminopmelate-aminotransferase (EC 2.6.1.17,
DapC, an enzyme of lysine biosynthesis) (see
MEDLINE:99175097).
Length = 379
Score = 26.6 bits (59), Expect = 7.9
Identities = 12/38 (31%), Positives = 16/38 (42%), Gaps = 8/38 (21%)
Query: 67 CHPKVKSAVREALEKFGTGAGGTRNISGNSLFHEKLEE 104
HPK+ A++E LEK N + E EE
Sbjct: 44 AHPKLVEALKEQLEKLV--------HVSNLYYTEPQEE 73
>gnl|CDD|215999 pfam00573, Ribosomal_L4, Ribosomal protein L4/L1 family. This
family includes Ribosomal L4/L1 from eukaryotes and
archaebacteria and L4 from eubacteria. L4 from yeast
has been shown to bind rRNA.
Length = 190
Score = 26.3 bits (59), Expect = 8.3
Identities = 11/17 (64%), Positives = 14/17 (82%)
Query: 22 KKRDHSYRVFKKVNRLA 38
K RD+SY++ KKV RLA
Sbjct: 77 KPRDYSYKLNKKVRRLA 93
>gnl|CDD|205373 pfam13192, Thioredoxin_3, Thioredoxin domain.
Length = 76
Score = 25.2 bits (56), Expect = 8.7
Identities = 10/23 (43%), Positives = 15/23 (65%), Gaps = 2/23 (8%)
Query: 63 LGMSCH--PKVKSAVREALEKFG 83
LG C PK++ AV+EA+ + G
Sbjct: 6 LGPGCAKCPKLEEAVKEAVAELG 28
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
0.319 0.134 0.389
Gapped
Lambda K H
0.267 0.0833 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,968,085
Number of extensions: 808621
Number of successful extensions: 907
Number of sequences better than 10.0: 1
Number of HSP's gapped: 899
Number of HSP's successfully gapped: 55
Length of query: 174
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 84
Effective length of database: 6,945,742
Effective search space: 583442328
Effective search space used: 583442328
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)