RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9442
(127 letters)
>gnl|CDD|214838 smart00827, PKS_AT, Acyl transferase domain in polyketide synthase
(PKS) enzymes.
Length = 298
Score = 69.0 bits (170), Expect = 5e-15
Identities = 26/62 (41%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 1 MAAVGLSWEEVK---ARAPADIVAACHNNVDSVTISGPPAAIDKFVAELSAEGVFAKKVA 57
M AVGLS EEV+ A P + A N+ SV +SG A+D+ A L AEG+FA+++
Sbjct: 128 MLAVGLSEEEVEPLLAGVPDRVSVAAVNSPSSVVLSGDEDAVDELAARLEAEGIFARRLK 187
Query: 58 SS 59
Sbjct: 188 VD 189
>gnl|CDD|144338 pfam00698, Acyl_transf_1, Acyl transferase domain.
Length = 319
Score = 64.0 bits (156), Expect = 4e-13
Identities = 27/61 (44%), Positives = 37/61 (60%), Gaps = 2/61 (3%)
Query: 1 MAAVGLSWEEVKARA--PADIVAACHNNVDSVTISGPPAAIDKFVAELSAEGVFAKKVAS 58
MAAVGL EEV+ A P +V A N+ SV ++GP A+D+FV + A GV A+ +A
Sbjct: 129 MAAVGLPAEEVEQLARWPDRVVVAIVNSPRSVVVAGPQEALDEFVERVEARGVRARVIAV 188
Query: 59 S 59
Sbjct: 189 D 189
>gnl|CDD|225858 COG3321, COG3321, Polyketide synthase modules and related proteins
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 1061
Score = 38.6 bits (90), Expect = 4e-04
Identities = 24/64 (37%), Positives = 33/64 (51%), Gaps = 4/64 (6%)
Query: 1 MAAVGLS-WEEVK---ARAPADIVAACHNNVDSVTISGPPAAIDKFVAELSAEGVFAKKV 56
M AV LS EV+ A + A N+ V I+G P AI +A L A+GV A+++
Sbjct: 656 MLAVELSLLAEVQELLALGRPQVPLAAVNSPQQVVIAGDPEAIAALIARLQAQGVRARRL 715
Query: 57 ASSG 60
A S
Sbjct: 716 AVSH 719
>gnl|CDD|223408 COG0331, FabD, (acyl-carrier-protein) S-malonyltransferase [Lipid
metabolism].
Length = 310
Score = 34.2 bits (79), Expect = 0.009
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 6/56 (10%)
Query: 1 MAAV-GLSWEEV-----KARAPADIVAACHNNVDSVTISGPPAAIDKFVAELSAEG 50
MAAV GL E+V +A + A +N+ + ISG A++K L G
Sbjct: 133 MAAVLGLDDEQVEKACEEAAQGTVVEIANYNSPGQIVISGTKEALEKAAEILKEAG 188
>gnl|CDD|188961 cd09562, SAM_liprin-alpha1,2,3,4_repeat1, SAM domain of
liprin-alpha1,2,3,4 proteins repeat 1. SAM (sterile
alpha motif) domain repeat 1 of liprin-alpha1,2,3,4
proteins is a protein-protein interaction domain.
Liprin-alpha proteins contain three copies (repeats) of
SAM domain. They may form heterodimers with liprin-beta
proteins through their SAM domains. Liprins were
originally identified as LAR (leukocyte common
antigen-related) transmembrane protein-tyrosine
phosphatase-interacting proteins. They participate in
mammary gland development and in axon guidance; in
particular, liprin-alpha is involved in formation of
the presynaptic active zone.
Length = 71
Score = 27.9 bits (62), Expect = 0.52
Identities = 12/27 (44%), Positives = 15/27 (55%)
Query: 6 LSWEEVKARAPADIVAACHNNVDSVTI 32
++W E+ PA VAAC NV S I
Sbjct: 10 VAWLELWVGMPAWYVAACRANVKSGAI 36
>gnl|CDD|240529 cd13124, MATE_SpoVB_like, Stage V sporulation protein B, also
known as Stage III sporulation protein F, and related
proteins. The integral membrane protein SpoVB has been
implicated in the biosynthesis of the peptidoglycan
component of the spore cortex in Bacillus subtilis.
This model represents a subfamily of the multidrug and
toxic compound extrusion (MATE)-like proteins. Proteins
from the MATE family are involved in exporting
metabolites across the cell membrane and are often
responsible for multidrug resistance (MDR).
Length = 434
Score = 28.2 bits (64), Expect = 1.1
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 29 SVTISGPPAAIDKFVAELSAEGVF--AKKVASSGF 61
++ +G P AI K VAE +A G + A+++
Sbjct: 45 TLATAGIPVAISKLVAEYNALGDYKGARRIFRVSL 79
>gnl|CDD|99809 cd06213, oxygenase_e_transfer_subunit, The oxygenase reductase
FAD/NADH binding domain acts as part of the
multi-component bacterial oxygenases which oxidize
hydrocarbons. Electron transfer is from NADH via FAD (in
the oxygenase reductase) and an [2FE-2S] ferredoxin
center (fused to the FAD/NADH domain and/or discrete) to
the oxygenase. Dioxygenases add both atoms of oxygen to
the substrate while mono-oxygenases add one atom to the
substrate and one atom to water. In dioxygenases, Class
I enzymes are 2 component, containing a reductase with
Rieske type [2Fe-2S] redox centers and an oxygenase.
Class II are 3 component, having discrete flavin and
ferredoxin proteins and an oxygenase. Class III have 2
[2Fe-2S] centers, one fused to the flavin domain and the
other separate.
Length = 227
Score = 27.7 bits (62), Expect = 1.4
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 34 GPPAAIDKFVAELSAEGVFAKKV 56
GPPA ID +A L A G+ + +
Sbjct: 200 GPPAMIDAAIAVLRALGIAREHI 222
>gnl|CDD|185268 PRK15370, PRK15370, E3 ubiquitin-protein ligase SlrP; Provisional.
Length = 754
Score = 27.4 bits (60), Expect = 2.3
Identities = 15/48 (31%), Positives = 26/48 (54%)
Query: 76 DTMLQFSILGINTRELYLPTRMQRVCIDPAKHKALVETLSGDKKTVPV 123
T L+ ILG+ T +P ++ + +D + K+L E L G+ KT+
Sbjct: 180 KTELRLKILGLTTIPACIPEQITTLILDNNELKSLPENLQGNIKTLYA 227
>gnl|CDD|132175 TIGR03131, malonate_mdcH, malonate decarboxylase, epsilon subunit.
Members of this protein family are the epsilon subunit
of malonate decarboxylase. This subunit has
malonyl-CoA/dephospho-CoA acyltransferase activity.
Malonate decarboxylase may be a soluble enzyme, or
linked to membrane subunits and active as a sodium pump.
The epsilon subunit is closely related to the malonyl
CoA-acyl carrier protein (ACP) transacylase family
described by TIGR00128, but acts on an ACP subunit of
malonate decarboxylase that has an unusual coenzyme A
derivative as its prothetic group.
Length = 295
Score = 27.3 bits (61), Expect = 2.5
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 2/59 (3%)
Query: 1 MAAVGLSWEEVKAR-APADIVAACHNNVDSVTISGPPAAIDKFVAELSAEGVF-AKKVA 57
+A +GL V+A A + A N D V I+G AA+ A G AK++A
Sbjct: 124 LAVLGLDLAAVEALIAKHGVYLAIINAPDQVVIAGSRAALRAVAELARAAGASRAKRLA 182
>gnl|CDD|220610 pfam10165, Ric8, Guanine nucleotide exchange factor synembryn.
Ric8 is involved in the EGL-30 neurotransmitter
signalling pathway. It is a guanine nucleotide exchange
factor that regulates neurotransmitter secretion.
Length = 439
Score = 27.3 bits (61), Expect = 2.7
Identities = 11/63 (17%), Positives = 25/63 (39%), Gaps = 17/63 (26%)
Query: 75 IDTMLQFSILGINTRE-----------------LYLPTRMQRVCIDPAKHKALVETLSGD 117
+DT+ + + L + L+L + +++ +D + L E L D
Sbjct: 24 LDTLARHAGLLSVVFDSPSEDVRREALKCLCNALFLSPKARQLFVDLGLGEGLAERLKED 83
Query: 118 KKT 120
++T
Sbjct: 84 EET 86
>gnl|CDD|221870 pfam12950, TaqI_C, TaqI-like C-terminal specificity domain. This
domain is found at the C-terminus of the TaqI protein
and is involved in DNA-binding and substrate
recognition.
Length = 118
Score = 26.4 bits (59), Expect = 3.2
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 63 GKLDWTGNWISYIDTMLQ 80
K+DW GN+I+Y LQ
Sbjct: 12 YKIDWEGNYINYDPKKLQ 29
>gnl|CDD|176809 cd08975, BaFpgNei_N_3, Uncharacterized bacterial subgroup of the
N-terminal domain of Fpg (formamidopyrimidine-DNA
glycosylase, MutM)_Nei (endonuclease VIII)
base-excision repair DNA glycosylases. This family is
an uncharacterized bacterial subgroup of the FpgNei_N
domain superfamily. DNA glycosylases maintain genome
integrity by recognizing base lesions created by
ionizing radiation, alkylating or oxidizing agents, and
endogenous reactive oxygen species. They initiate the
base-excision repair process, which is completed with
the help of enzymes such as phosphodiesterases, AP
endonucleases, DNA polymerases and DNA ligases. DNA
glycosylases cleave the N-glycosyl bond between the
sugar and the damaged base, creating an AP
(apurinic/apyrimidinic) site. Most FpgNei DNA
glycosylases use their N-terminal proline residue as the
key catalytic nucleophile, and the reaction proceeds via
a Schiff base intermediate. One exception is mouse
Nei-like glycosylase 3 (Neil3) which forms a Schiff base
intermediate via its N-terminal valine. In this family
the N-terminal proline is replaced by an isoleucine or
valine. Escherichia coli Fpg prefers
8-oxo-7,8-dihydroguanine (8-oxoG) and oxidized purines
and Escherichia coli Nei recognizes oxidized
pyrimidines. However, neither Escherichia coli Fpg or
Nei belong to this family. In addition to this
BaFpgNei_N_3 domain, enzymes belonging to this family
contain a helix-two turn-helix (H2TH) domain and a
zinc-finger motif.
Length = 117
Score = 26.1 bits (58), Expect = 3.6
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 13/74 (17%)
Query: 54 KKVASS-GFTGKLDWTGNWISYIDTMLQFSILGINTRELYLPTRMQRVCIDPAKHKALVE 112
K++ S+ GF G ++ I + D L F+ G+N R Y ++ P K++ L+E
Sbjct: 51 KRITSAEGFGGFVE-----IIFEDKRLLFND-GVNVRYYYGGEKI------PKKYQLLIE 98
Query: 113 TLSGDKKTVPVAMY 126
VAMY
Sbjct: 99 FDDDSFLVFTVAMY 112
>gnl|CDD|222969 PHA03067, PHA03067, hypothetical protein; Provisional.
Length = 383
Score = 26.5 bits (59), Expect = 4.8
Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 7/44 (15%)
Query: 18 DIVAACHNNVDSVT-ISGPPA------AIDKFVAELSAEGVFAK 54
+I A N +D +T I A D F+ ++ G F K
Sbjct: 288 EIKCASRNGIDFITHIDNKRLDTILIIAKDDFLKNVTFSGTFKK 331
>gnl|CDD|234052 TIGR02900, spore_V_B, stage V sporulation protein B. SpoVB is
the stage V sporulation protein B of the bacterial
endopore formation program in Bacillus subtilis and
various other Firmcutes. It is nearly universal among
endospore-formers. Paralogs with rather high sequence
similarity to SpoVB exist, including YkvU in B.
subtilis and a number of proteins in the genus
Clostridium. Member sequences for the seed alignment
were chosen to select those proteins, no more than one
to a genome, closest to B. subtilis SpoVB in a neighbor
joining tree [Cellular processes, Sporulation and
germination].
Length = 488
Score = 26.1 bits (58), Expect = 6.0
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 29 SVTISGPPAAIDKFVAELSAEG 50
++T G P AI KFVAE SA+
Sbjct: 50 TLTTGGLPVAISKFVAEASAKN 71
>gnl|CDD|234009 TIGR02779, NHEJ_ligase_lig, DNA polymerase LigD, ligase domain.
DNA repair of double-stranded breaks by non-homologous
end joining (NHEJ) is accomplished by a two-protein
system that is present in a minority of prokaryotes. One
component is the Ku protein (see TIGR02772), which binds
DNA ends. The other is a DNA ligase, a protein that is a
multidomain polypeptide in most of those bacteria that
have NHEJ, a permuted polypeptide in Mycobacterium
tuberculosis and a few other species, and the product of
tandem genes in some other bacteria. This model
represents the ligase domain.
Length = 298
Score = 25.7 bits (57), Expect = 7.7
Identities = 15/43 (34%), Positives = 19/43 (44%), Gaps = 5/43 (11%)
Query: 29 SVTISGPPAAIDKFVAELSAEGVFAKKVAS---SGFTGKLDWT 68
SV G A+ + L EGV AK+ S SG + DW
Sbjct: 139 SVHFEGDGQALLEAACRLGLEGVVAKRRDSPYRSGRSA--DWL 179
>gnl|CDD|132348 TIGR03305, alt_F1F0_F1_bet, alternate F1F0 ATPase, F1 subunit beta.
A small number of taxonomically diverse prokaryotic
species have what appears to be a second ATP synthase,
in addition to the normal F1F0 ATPase in bacteria and
A1A0 ATPase in archaea. These enzymes use ion gradients
to synthesize ATP, and in principle may run in either
direction. This model represents the F1 beta subunit of
this apparent second ATP synthase.
Length = 449
Score = 25.6 bits (56), Expect = 8.4
Identities = 13/31 (41%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 36 PAAIDKFVAELSAEGVFAKKVASSGFTGKLD 66
PAA+ F + LSA V ++K AS G +D
Sbjct: 303 PAAVHTF-SHLSASLVLSRKRASEGLYPAID 332
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 0.132 0.395
Gapped
Lambda K H
0.267 0.0893 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,488,860
Number of extensions: 563093
Number of successful extensions: 522
Number of sequences better than 10.0: 1
Number of HSP's gapped: 520
Number of HSP's successfully gapped: 31
Length of query: 127
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 42
Effective length of database: 7,167,512
Effective search space: 301035504
Effective search space used: 301035504
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: 53 (23.9 bits)