RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11963
(172 letters)
>gnl|CDD|238429 cd00833, PKS, polyketide synthases (PKSs) polymerize simple fatty
acids into a large variety of different products, called
polyketides, by successive decarboxylating Claisen
condensations. PKSs can be divided into 2 groups,
modular type I PKSs consisting of one or more large
multifunctional proteins and iterative type II PKSs,
complexes of several monofunctional subunits.
Length = 421
Score = 121 bits (305), Expect = 4e-33
Identities = 44/114 (38%), Positives = 69/114 (60%)
Query: 56 YAFNFSGLYGAPSRTGKIKDIASFDAEFFGIHSKLANVMDPQLRMLLELTHESIMDGGFN 115
Y R G + D+ +FDA FFGI + A MDPQ R+LLE+ E++ D G++
Sbjct: 46 YPDPGKPGKTYTRRGGFLDDVDAFDAAFFGISPREAEAMDPQQRLLLEVAWEALEDAGYS 105
Query: 116 PEELRGTRTGVYIGLMTTEANDFAEGNPEKLTGYETIGSTRAMLANRLSYAFNF 169
PE L G+RTGV++G +++ + +P+++ Y G++RA LANR+SY F+
Sbjct: 106 PESLAGSRTGVFVGASSSDYLELLARDPDEIDAYAATGTSRAFLANRISYFFDL 159
Score = 71.8 bits (177), Expect = 3e-15
Identities = 24/61 (39%), Positives = 41/61 (67%)
Query: 2 DGGFNPEELRGTRTGVYIGLMTTEANDFAEGNPEKLTGYETIGSTRAMLANRLSYAFNFS 61
D G++PE L G+RTGV++G +++ + +P+++ Y G++RA LANR+SY F+
Sbjct: 101 DAGYSPESLAGSRTGVFVGASSSDYLELLARDPDEIDAYAATGTSRAFLANRISYFFDLR 160
Query: 62 G 62
G
Sbjct: 161 G 161
>gnl|CDD|225858 COG3321, COG3321, Polyketide synthase modules and related proteins
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 1061
Score = 102 bits (256), Expect = 7e-26
Identities = 43/145 (29%), Positives = 67/145 (46%), Gaps = 7/145 (4%)
Query: 33 NPEKL--TGYETIGSTRAMLANRLSYAFNFSGLYGAPSRT-----GKIKDIASFDAEFFG 85
+PE+ E + A+R + P ++ G + D+ FDA FFG
Sbjct: 20 SPEEFWDLLKEGRDEITEVPADRWDVDAYYDPDPTVPGKSYSRWGGFLDDVDDFDALFFG 79
Query: 86 IHSKLANVMDPQLRMLLELTHESIMDGGFNPEELRGTRTGVYIGLMTTEANDFAEGNPEK 145
I + A MDPQ R+LLE+ E++ D G P+ LRG+ TGV+ G + + E
Sbjct: 80 ISPREAEAMDPQQRLLLEVAWEALEDAGIYPDSLRGSATGVFAGASVADYLLLLLADDEA 139
Query: 146 LTGYETIGSTRAMLANRLSYAFNFS 170
Y G++ ++ A R+SY S
Sbjct: 140 EPEYAITGNSSSVAAGRISYVLGLS 164
Score = 54.0 bits (130), Expect = 5e-09
Identities = 19/61 (31%), Positives = 29/61 (47%)
Query: 2 DGGFNPEELRGTRTGVYIGLMTTEANDFAEGNPEKLTGYETIGSTRAMLANRLSYAFNFS 61
D G P+ LRG+ TGV+ G + + E Y G++ ++ A R+SY S
Sbjct: 105 DAGIYPDSLRGSATGVFAGASVADYLLLLLADDEAEPEYAITGNSSSVAAGRISYVLGLS 164
Query: 62 G 62
G
Sbjct: 165 G 165
>gnl|CDD|214836 smart00825, PKS_KS, Beta-ketoacyl synthase. The structure of
beta-ketoacyl synthase is similar to that of the
thiolase family and also chalcone synthase. The active
site of beta-ketoacyl synthase is located between the N
and C-terminal domains.
Length = 298
Score = 95.1 bits (238), Expect = 3e-24
Identities = 30/63 (47%), Positives = 45/63 (71%)
Query: 72 KIKDIASFDAEFFGIHSKLANVMDPQLRMLLELTHESIMDGGFNPEELRGTRTGVYIGLM 131
+ D+ FDA FFGI + A MDPQ R+LLE+ E++ D G +PE LRG+RTGV++G+
Sbjct: 26 GLDDVDLFDAAFFGISPREAEAMDPQQRLLLEVAWEALEDAGIDPESLRGSRTGVFVGVS 85
Query: 132 TTE 134
+++
Sbjct: 86 SSD 88
Score = 40.0 bits (95), Expect = 2e-04
Identities = 12/24 (50%), Positives = 20/24 (83%)
Query: 2 DGGFNPEELRGTRTGVYIGLMTTE 25
D G +PE LRG+RTGV++G+ +++
Sbjct: 65 DAGIDPESLRGSRTGVFVGVSSSD 88
>gnl|CDD|215723 pfam00109, ketoacyl-synt, Beta-ketoacyl synthase, N-terminal
domain. The structure of beta-ketoacyl synthase is
similar to that of the thiolase family (pfam00108) and
also chalcone synthase. The active site of beta-ketoacyl
synthase is located between the N and C-terminal
domains. The N-terminal domain contains most of the
structures involved in dimer formation and also the
active site cysteine.
Length = 243
Score = 87.3 bits (217), Expect = 2e-21
Identities = 40/114 (35%), Positives = 58/114 (50%), Gaps = 6/114 (5%)
Query: 61 SGLYGAPSRTGKIKDIASFDAEFFGIHSKLANVMDPQLRMLLELTHESIMDGGFNPEELR 120
SGLY G+I FDA FFGI + A MDPQ R+ LE E++ D G +P LR
Sbjct: 41 SGLYPPSRVAGEIYG-FDFDAAFFGISPREAEAMDPQQRLALEAAWEALEDAGLDPASLR 99
Query: 121 GTR-TGVYIGLMTTEANDFA----EGNPEKLTGYETIGSTRAMLANRLSYAFNF 169
G+ TGV++G + + + G P +++ Y T ++ A R+SY
Sbjct: 100 GSDRTGVFVGSGSGDYAELQALDSAGGPRRVSPYLTGAWMPSVAAGRISYRLGL 153
Score = 46.9 bits (112), Expect = 9e-07
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 5/66 (7%)
Query: 2 DGGFNPEELRGTR-TGVYIGLMTTEANDFA----EGNPEKLTGYETIGSTRAMLANRLSY 56
D G +P LRG+ TGV++G + + + G P +++ Y T ++ A R+SY
Sbjct: 90 DAGLDPASLRGSDRTGVFVGSGSGDYAELQALDSAGGPRRVSPYLTGAWMPSVAAGRISY 149
Query: 57 AFNFSG 62
G
Sbjct: 150 RLGLRG 155
>gnl|CDD|238421 cd00825, decarbox_cond_enzymes, decarboxylating condensing enzymes;
Family of enzymes that catalyze the formation of a new
carbon-carbon bond by a decarboxylating Claisen-like
condensation reaction. Members are involved in the
synthesis of fatty acids and polyketides, a diverse
group of natural products. Both pathways are an
iterative series of additions of small carbon units,
usually acetate, to a nascent acyl group. There are 2
classes of decarboxylating condensing enzymes, which can
be distinguished by sequence similarity, type of active
site residues and type of primer units (acetyl CoA or
acyl carrier protein (ACP) linked units).
Length = 332
Score = 36.5 bits (84), Expect = 0.004
Identities = 10/75 (13%), Positives = 21/75 (28%), Gaps = 2/75 (2%)
Query: 99 RMLLELTHESIMDGGFNPEELRGTRTGVYIGLMTT--EANDFAEGNPEKLTGYETIGSTR 156
+ E +I D G + E + GV +G F + Y +
Sbjct: 13 ILGFEAAERAIADAGLSREYQKNPIVGVVVGTGGGSPRFQVFGADAMRAVGPYVVTKAMF 72
Query: 157 AMLANRLSYAFNFSV 171
+ +++
Sbjct: 73 PGASGQIATPLGIHG 87
>gnl|CDD|223381 COG0304, FabB, 3-oxoacyl-(acyl-carrier-protein) synthase [Lipid
metabolism / Secondary metabolites biosynthesis,
transport, and catabolism].
Length = 412
Score = 32.6 bits (75), Expect = 0.082
Identities = 18/70 (25%), Positives = 26/70 (37%), Gaps = 13/70 (18%)
Query: 73 IKDIASFDAEFFGIHS-------------KLANVMDPQLRMLLELTHESIMDGGFNPEEL 119
I+ I FDA G+ K MD ++ + E++ D G + E
Sbjct: 34 IRPITRFDASGLGVKIAGEIKDLDDQIAKKERRFMDRFSQLAVVAAVEALEDAGLDNELN 93
Query: 120 RGTRTGVYIG 129
R GV IG
Sbjct: 94 VDMRVGVAIG 103
>gnl|CDD|200247 TIGR03150, fabF, beta-ketoacyl-acyl-carrier-protein synthase II.
3-oxoacyl-[acyl-carrier-protein] synthase 2 (KAS-II,
FabF) is involved in the condensation step of fatty acid
biosynthesis in which the malonyl donor group is
decarboxylated and the resulting carbanion used to
attack and extend the acyl group attached to the acyl
carrier protein. Most genomes encoding fatty acid
biosynthesis contain a number of condensing enzymes,
often of all three types: 1, 2 and 3. Synthase 2 is
mechanistically related to synthase 1 (KAS-I, FabB)
containing a number of absolutely conserved catalytic
residues in common. This model is based primarily on
genes which are found in apparent operons with other
essential genes of fatty acid biosynthesis
(GenProp0681). The large gap between the trusted cutoff
and the noise cutoff contains many genes which are not
found adjacent to genes of the fatty acid pathway in
genomes that often also contain a better hit to this
model. These genes may be involved in other processes
such as polyketide biosyntheses. Some genomes contain
more than one above-trusted hit to this model which may
result from recent paralogous expansions. Second hits to
this model which are not next to other fatty acid
biosynthesis genes may be involved in other processes.
FabB sequences should fall well below the noise cutoff
of this model [Fatty acid and phospholipid metabolism,
Biosynthesis].
Length = 407
Score = 32.1 bits (74), Expect = 0.11
Identities = 22/59 (37%), Positives = 30/59 (50%), Gaps = 4/59 (6%)
Query: 71 GKIKDIASFDAEFFGIHSKLANVMDPQLRMLLELTHESIMDGGFNPEELRGTRTGVYIG 129
G++KD FD E + I K A MD ++ L E++ D G + EE R GV IG
Sbjct: 49 GEVKD---FDPEDY-IDKKEARRMDRFIQYALAAAKEAVEDSGLDIEEEDAERVGVIIG 103
>gnl|CDD|238430 cd00834, KAS_I_II, Beta-ketoacyl-acyl carrier protein (ACP)
synthase (KAS), type I and II. KASs are responsible for
the elongation steps in fatty acid biosynthesis. KASIII
catalyses the initial condensation and KAS I and II
catalyze further elongation steps by Claisen
condensation of malonyl-acyl carrier protein (ACP) with
acyl-ACP.
Length = 406
Score = 32.1 bits (74), Expect = 0.11
Identities = 24/76 (31%), Positives = 30/76 (39%), Gaps = 16/76 (21%)
Query: 69 RTGKIKDIASFDAEFFGIH---------------SKLANVMDPQLRMLLELTHESIMDGG 113
R+G I+ I FDA F K MD + L E++ D G
Sbjct: 29 RSG-IRPITRFDASGFPSRIAGEVPDFDPEDYLDRKELRRMDRFAQFALAAAEEALADAG 87
Query: 114 FNPEELRGTRTGVYIG 129
+PEEL R GV IG
Sbjct: 88 LDPEELDPERIGVVIG 103
Score = 27.1 bits (61), Expect = 5.3
Identities = 19/68 (27%), Positives = 28/68 (41%), Gaps = 7/68 (10%)
Query: 2 DGGFNPEELRGTRTGVYIG-----LMTTEAND--FAEGNPEKLTGYETIGSTRAMLANRL 54
D G +PEEL R GV IG L T E E P +++ + + M A ++
Sbjct: 85 DAGLDPEELDPERIGVVIGSGIGGLATIEEAYRALLEKGPRRVSPFFVPMALPNMAAGQV 144
Query: 55 SYAFNFSG 62
+ G
Sbjct: 145 AIRLGLRG 152
>gnl|CDD|236267 PRK08451, PRK08451, DNA polymerase III subunits gamma and tau;
Validated.
Length = 535
Score = 31.2 bits (71), Expect = 0.29
Identities = 14/33 (42%), Positives = 22/33 (66%), Gaps = 2/33 (6%)
Query: 35 EKLTGYETIGST--RAMLANRLSYAFNFSGLYG 65
++L G E++ T A+ NRL++A+ FSGL G
Sbjct: 14 DELIGQESVSKTLSLALDNNRLAHAYLFSGLRG 46
>gnl|CDD|236265 PRK08439, PRK08439, 3-oxoacyl-(acyl carrier protein) synthase II;
Reviewed.
Length = 406
Score = 30.5 bits (69), Expect = 0.42
Identities = 28/86 (32%), Positives = 38/86 (44%), Gaps = 24/86 (27%)
Query: 73 IKDIASFDAEFFGIHSKLA---------NVMDPQ--------LRMLLELTHESIMDGGFN 115
IK I FDA F + ++A VMDP+ +++ L+ E++ D GF
Sbjct: 33 IKKITLFDASDFPV--QIAGEITDFDPTEVMDPKEVKKADRFIQLGLKAAREAMKDAGFL 90
Query: 116 PEELRGTRTGVYI-----GLMTTEAN 136
PEEL R GV GL E N
Sbjct: 91 PEELDAERFGVSSASGIGGLPNIEKN 116
>gnl|CDD|215421 PLN02787, PLN02787, 3-oxoacyl-[acyl-carrier-protein] synthase II.
Length = 540
Score = 29.2 bits (65), Expect = 1.2
Identities = 23/67 (34%), Positives = 35/67 (52%), Gaps = 8/67 (11%)
Query: 67 PSR-TGKIKDIASFDAEFFGIHSKLANVMDPQLRMLLELTHESIMDGGFNPE---ELRGT 122
P+R G+IK SF + + + KL+ MD + LL +++ DGG + EL T
Sbjct: 172 PTRIAGEIK---SFSTDGW-VAPKLSKRMDKFMLYLLTAGKKALADGGITEDVMKELDKT 227
Query: 123 RTGVYIG 129
+ GV IG
Sbjct: 228 KCGVLIG 234
>gnl|CDD|235987 PRK07314, PRK07314, 3-oxoacyl-(acyl carrier protein) synthase II;
Reviewed.
Length = 411
Score = 29.0 bits (66), Expect = 1.2
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 4/59 (6%)
Query: 71 GKIKDIASFDAEFFGIHSKLANVMDPQLRMLLELTHESIMDGGFNPEELRGTRTGVYIG 129
G++KD F+ + + + K A MD ++ + +++ D G E R GV IG
Sbjct: 50 GEVKD---FNPDDY-MSRKEARRMDRFIQYGIAAAKQAVEDAGLEITEENADRIGVIIG 104
>gnl|CDD|130074 TIGR01001, metA, homoserine O-succinyltransferase. The apparent
equivalog from Bacillus subtilis is broken into two
tandem reading frames [Amino acid biosynthesis,
Aspartate family].
Length = 300
Score = 28.3 bits (63), Expect = 1.9
Identities = 24/96 (25%), Positives = 34/96 (35%), Gaps = 25/96 (26%)
Query: 63 LYGAP--SRTGKI-----KDIAS-------FDAEFFGIHSKLANVMDPQLRMLLELTHES 108
YG P + K+ DIA FD F HS+ A+ + + +L
Sbjct: 152 FYGIPKYTLPEKLSGVYKHDIAPDSLLLRGFDDFFLAPHSRYADFDAEDIDKVTDL---E 208
Query: 109 IMDGGFNPEELRGTRTGVYIGLMTTEANDFAEGNPE 144
I+ GVY+ E N F G+PE
Sbjct: 209 IL--------AESDEAGVYLAANKDERNIFVTGHPE 236
>gnl|CDD|238424 cd00828, elong_cond_enzymes, "elongating" condensing enzymes are a
subclass of decarboxylating condensing enzymes,
including beta-ketoacyl [ACP] synthase, type I and II
and polyketide synthases.They are characterized by the
utlization of acyl carrier protein (ACP) thioesters as
primer substrates, as well as the nature of their active
site residues.
Length = 407
Score = 28.2 bits (63), Expect = 2.4
Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 93 VMDPQLRMLLELTHESIMDGGFN-PEELRGTRTGVYIG 129
++D + L T E++ D G P E+ + GV +G
Sbjct: 68 IVDRTTLLALVATEEALADAGITDPYEVHPSEVGVVVG 105
>gnl|CDD|219473 pfam07580, Peptidase_M26_C, M26 IgA1-specific Metallo-endopeptidase
C-terminal region. These peptidases, which cleave
mammalian IgA, are found in Gram-positive bacteria.
Often found associated with pfam00746, they may be
attached to the cell wall.
Length = 731
Score = 27.3 bits (61), Expect = 5.4
Identities = 27/107 (25%), Positives = 38/107 (35%), Gaps = 32/107 (29%)
Query: 56 YAFNFSGLYGAPSRTGKIKDIASFDAEFFGIHSKLANVMDPQLRMLLELTHESIMDGGFN 115
Y F + + IKD+ F +FFG K +V+D L+E I G N
Sbjct: 121 YDFKYGDM--------NIKDLMMFKPDFFG---KNVSVLD----RLIE-----IGKSGEN 160
Query: 116 PEELRGTRT--------GVYIGLMTTEANDFAEGNPEKLTGYETIGS 154
L+G+ G T + DF E N + T T
Sbjct: 161 --NLKGSNNVEAYREVLAKNTG--TGDLFDFLEYNRKLFTPETTNNE 203
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.317 0.136 0.389
Gapped
Lambda K H
0.267 0.0940 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,083,423
Number of extensions: 840651
Number of successful extensions: 651
Number of sequences better than 10.0: 1
Number of HSP's gapped: 649
Number of HSP's successfully gapped: 27
Length of query: 172
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 82
Effective length of database: 6,945,742
Effective search space: 569550844
Effective search space used: 569550844
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (24.6 bits)