RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5605
(152 letters)
>gnl|CDD|144617 pfam01090, Ribosomal_S19e, Ribosomal protein S19e.
Length = 140
Score = 203 bits (520), Expect = 8e-69
Identities = 67/120 (55%), Positives = 86/120 (71%)
Query: 13 KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
KSGK+KVPEW D VK+ KEL P DPDW+Y R A++ R +Y+R PVGV + KI+GGRK
Sbjct: 21 KSGKIKVPEWADFVKTGVHKELPPEDPDWWYVRAASILRKLYLRGPVGVGRLRKIYGGRK 80
Query: 73 RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
R GV PSHF + SGS+ RKALQ LE+ ++EK GGR++T GR D+DRIAA++
Sbjct: 81 RRGVRPSHFVKGSGSIIRKALQQLEKAGLVEKDPKGGRRLTPQGRSDLDRIAAEVLKELA 140
>gnl|CDD|225147 COG2238, RPS19A, Ribosomal protein S19E (S16A) [Translation,
ribosomal structure and biogenesis].
Length = 147
Score = 150 bits (382), Expect = 1e-47
Identities = 54/124 (43%), Positives = 77/124 (62%), Gaps = 1/124 (0%)
Query: 14 SGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKR 73
+GK+K PEW DIVK+ KE P DW+Y R A++ R IY+ PVG++ + +GGRK
Sbjct: 23 TGKVKPPEWADIVKTGVHKERPPEQEDWWYVRAASILRKIYIDGPVGIERLRTAYGGRKN 82
Query: 74 NGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKE 133
G P F + SGS+ RK LQ LE+ ++EK+ GR +T GR +DRIA +I+ +E
Sbjct: 83 RGSRPEKFRKGSGSIIRKVLQQLEKAGLVEKT-PKGRVLTPKGRSLLDRIATEIKEELEE 141
Query: 134 AALQ 137
L+
Sbjct: 142 PELE 145
>gnl|CDD|236470 PRK09333, PRK09333, 30S ribosomal protein S19e; Provisional.
Length = 150
Score = 134 bits (341), Expect = 2e-41
Identities = 53/123 (43%), Positives = 74/123 (60%), Gaps = 4/123 (3%)
Query: 13 KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
++K PEW VK+ KE P DW+Y R A++ R +Y+ PVGV+ + +GGRK
Sbjct: 22 NVDEIKPPEWAAFVKTGVHKERPPEQEDWWYVRAASILRKVYIDGPVGVERLRTAYGGRK 81
Query: 73 RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
GV P HF + SGS+ RK LQ LE+ ++EK+ GR IT GR +D +AA++ KK
Sbjct: 82 NRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTKK-GRVITPKGRSLLDNLAAEV---KK 137
Query: 133 EAA 135
E A
Sbjct: 138 ELA 140
>gnl|CDD|140127 PTZ00095, PTZ00095, 40S ribosomal protein S19; Provisional.
Length = 169
Score = 121 bits (304), Expect = 1e-35
Identities = 46/122 (37%), Positives = 72/122 (59%), Gaps = 1/122 (0%)
Query: 15 GKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRN 74
GK+ VP+ +IVK++ +ELAP +PDW+Y RCAA+ R +Y+R VG + K F +KR
Sbjct: 48 GKIFVPKCTEIVKTSHGRELAPQNPDWYYIRCAAVLRALYLRPDVGYGGLRKRFSSKKRR 107
Query: 75 GVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG-GRKITSHGRRDMDRIAAQIRVSKKE 133
G P+H R+SG + R Q LE++ ++E+ GR++T G + A Q+ + K
Sbjct: 108 GSAPNHTVRASGKILRWICQQLEKLGLVEQGPKKKGRRLTRKGCNFANAFARQVTIRKFG 167
Query: 134 AA 135
Sbjct: 168 KE 169
>gnl|CDD|212083 cd11514, SLC6sbd_DAT1, Na(+)- and Cl(-)-dependent dopamine
transporter 1; solute-binding domain. DAT1 (also called
DAT), is a plasma membrane transport protein that
functions at the dopaminergic synapses to transport
dopamine from the extracellular space back into the
presynaptic nerve terminal. Human DAT1 is encoded by the
SLC6A3 gene, and is expressed in the brain. DAT1 may
play a role in diseases or disorders related to
dopaminergic neurons, including attention-deficit
hyperactivity disorder (ADHD), Tourette syndrome,
Parkinson's disease, alcoholism, drug abuse,
schizophrenia, extraversion, and risky behavior. This
subgroup belongs to the solute carrier 6 (SLC6)
transporter family.
Length = 555
Score = 29.5 bits (66), Expect = 0.68
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 1 MVSVSYIGFRPSKSGKMKVPEWVDIV 26
+V VS + FRP K G P+W ++V
Sbjct: 476 VVVVSIVTFRPPKYGSYIFPDWANMV 501
>gnl|CDD|223708 COG0635, HemN, Coproporphyrinogen III oxidase and related Fe-S
oxidoreductases [Coenzyme metabolism].
Length = 416
Score = 29.2 bits (66), Expect = 0.77
Identities = 16/63 (25%), Positives = 23/63 (36%), Gaps = 5/63 (7%)
Query: 67 IFGGRKRNGVCPSHFCRSSG----SVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDR 122
I G R GV + G + + L L ++E D R +T GR +
Sbjct: 346 ILGLRLNFGVDLAELEERFGIFKFAEILELLAELIADGLLELDGDRLR-LTEKGRLLLRS 404
Query: 123 IAA 125
IA
Sbjct: 405 IAE 407
>gnl|CDD|132002 TIGR02957, SigX4, RNA polymerase sigma-70 factor, TIGR02957 family.
This group of sigma factors are members of the sigma-70
family (TIGR02937). They and appear by homology, tree
building and bidirectional best hits, to represent a
conserved family. This family is found in a limited
number of bacterial lineages. This family includes
apparent paralogous expansion in Streptomyces coelicolor
A3(2), and multiple copies in Mycobacterium smegmatis
MC2, Streptomyces avermitilis MA-4680 and Nocardia
farcinica IFM10152.
Length = 281
Score = 28.9 bits (65), Expect = 1.1
Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 101 IIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAALQALAAQGITVVPTG 150
I+ KS+ R++ S RR +D + VS++E+ + L + + TG
Sbjct: 133 IVGKSEANCRQLVSRARRHLDARRPRFEVSREES--RQLLERFVEAAQTG 180
>gnl|CDD|153080 cd00365, HMG-CoA_reductase, Hydroxymethylglutaryl-coenzyme A
(HMG-CoA) reductase (HMGR).
Hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase
(HMGR) is a tightly regulated enzyme, which catalyzes
the synthesis of coenzyme A and mevalonate in isoprenoid
synthesis. In mammals, this is the rate limiting
committed step in cholesterol biosynthesis. Bacteria,
such as Pseudomonas mevalonii, which rely solely on
mevalonate for their carbon source, catalyze the reverse
reaction, using an NAD-dependent HMGR to deacetylate
mevalonate into 3-hydroxy-3-methylglutaryl-CoA. There
are two classes of HMGR: class I enzymes which are found
predominantly in eukaryotes and contain N-terminal
membrane regions and class II enzymes which are found
primarily in prokaryotes and are soluble as they lack
the membrane region. With the exception of Archaeoglobus
fulgidus, most archeae are assigned to class I, based on
sequence similarity of the active site, even though they
lack membrane regions. Yeast and human HMGR are
divergent in their N-terminal regions, but are conserved
in their active site. In contrast, human and bacterial
HMGR differ in their active site architecture. While the
prokaryotic enzyme is a homodimer, the eukaryotic enzyme
is a homotetramer.
Length = 376
Score = 28.0 bits (62), Expect = 2.1
Identities = 10/35 (28%), Positives = 20/35 (57%)
Query: 110 RKITSHGRRDMDRIAAQIRVSKKEAALQALAAQGI 144
R + + + RIA + +++ A++ALA +GI
Sbjct: 333 RILGVKTAQALARIAVAVGLAQNLGAMRALATEGI 367
>gnl|CDD|224639 COG1725, COG1725, Predicted transcriptional regulators
[Transcription].
Length = 125
Score = 27.2 bits (61), Expect = 2.3
Identities = 12/57 (21%), Positives = 28/57 (49%)
Query: 89 ARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAALQALAAQGIT 145
++A Q LE+ I+E G +T + +D++ ++ + E ++ A G++
Sbjct: 52 VQRAYQELEREGIVETKRGKGTFVTEDAKEILDQLKRELAEEELEEFIEEAKALGLS 108
>gnl|CDD|130775 TIGR01714, phage_rep_org_N, phage replisome organizer, putative,
N-terminal region. This model represents the N-terminal
domain of a small family of phage proteins. The protein
contains a region of low-complexity sequence that
reflects DNA direct repeats able to function as an
origin of phage replication. The region covered by this
model is N-terminal to the low-complexity region [Mobile
and extrachromosomal element functions, Prophage
functions].
Length = 119
Score = 27.1 bits (60), Expect = 2.3
Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 5/58 (8%)
Query: 81 FCRSSGSVARKALQALEQVNIIEKSDDGGRKITS----HGRRDMDRIAAQIRVSKKEA 134
F R+ G + R LQ LE + +IEK ++G + + G + ++A
Sbjct: 61 FNRNVGDI-RITLQTLESLGLIEKKNNGDIFLENWEKHVGSDSASARRERKFRRNQKA 117
>gnl|CDD|235498 PRK05541, PRK05541, adenylylsulfate kinase; Provisional.
Length = 176
Score = 27.3 bits (61), Expect = 2.7
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 6/66 (9%)
Query: 87 SVARKALQALEQV--NIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAALQA-LAAQG 143
++A+ + L+ N+I D R+I H D ++I ++ K A L LA QG
Sbjct: 22 TIAKALYERLKLKYSNVIYLDGDELREILGHYGYDKQ---SRIEMALKRAKLAKFLADQG 78
Query: 144 ITVVPT 149
+ V+ T
Sbjct: 79 MIVIVT 84
>gnl|CDD|188414 TIGR03899, TIGR03899, TIGR03899 family protein. Members of this
protein family are conserved hypothetical proteins with
a limited species distribution within the
Gammaproteobacteria. It is common in the genera Vibrio
and Shewanella, and in this resembles the C-terminal
domain and putative protein sorting motif TIGR03501.
This model, but design, does not extend to all
homologs,but rather represents a particular clade.
Length = 250
Score = 27.2 bits (61), Expect = 3.0
Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 38 DPDWFYTRCAALARHIYMRS 57
DPDW Y R +A I+ RS
Sbjct: 59 DPDWLY-RFFQMAEDIHNRS 77
>gnl|CDD|222732 pfam14394, DUF4423, Domain of unknown function (DUF4423). This
presumed domain is functionally uncharacterized. This
domain family is found in bacteria, and is approximately
170 amino acids in length.
Length = 171
Score = 26.8 bits (60), Expect = 3.8
Identities = 8/26 (30%), Positives = 15/26 (57%)
Query: 89 ARKALQALEQVNIIEKSDDGGRKITS 114
R +L+ LE++ +++K DG T
Sbjct: 58 VRDSLEFLEKLGLLKKDGDGNYVQTD 83
>gnl|CDD|236454 PRK09288, purT, phosphoribosylglycinamide formyltransferase 2;
Validated.
Length = 395
Score = 27.0 bits (61), Expect = 4.2
Identities = 8/16 (50%), Positives = 9/16 (56%)
Query: 134 AALQALAAQGITVVPT 149
AL L +G VVPT
Sbjct: 89 DALVELEKEGFNVVPT 104
>gnl|CDD|222024 pfam13282, DUF4070, Domain of unknown function (DUF4070). This
is a bacterial domain often found at the C-terminus of
Radical_SAM methylases.
Length = 146
Score = 26.4 bits (59), Expect = 5.3
Identities = 9/50 (18%), Positives = 16/50 (32%), Gaps = 7/50 (14%)
Query: 21 EWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGG 70
E+ D F L Y+P+ + R P K+ + +
Sbjct: 40 EYRDA-----FWTL--YEPEAYLDRVYRQFLEYGPPRPPKFKSPQRSWKD 82
>gnl|CDD|236000 PRK07360, PRK07360, FO synthase subunit 2; Reviewed.
Length = 371
Score = 26.8 bits (60), Expect = 5.4
Identities = 8/15 (53%), Positives = 12/15 (80%)
Query: 15 GKMKVPEWVDIVKSA 29
K+K EW++IVK+A
Sbjct: 196 EKIKTAEWIEIVKTA 210
>gnl|CDD|239493 cd03399, Band_7_flotillin, Band_7_flotillin: a subgroup of the band
7 domain of flotillin (reggie) like proteins. This
subgroup contains proteins similar to stomatin,
prohibitin, flotillin, HlfK/C and podicin. These two
proteins are lipid raft-associated. Individual proteins
of this band 7 domain family may cluster to form
membrane microdomains which may in turn recruit
multiprotein complexes. Microdomains formed from
flotillin proteins may in addition be dynamic units with
their own regulatory functions. Flotillins have been
implicated in signal transduction, vesicle trafficking,
cytoskeleton rearrangement and, interact with a variety
of proteins. Flotillins may play a role in the
progression of prion disease, in the pathogenesis of
neurodegenerative diseases such as Parkinson's and
Alzheimer's disease and, in cancer invasion and
metastasis.
Length = 128
Score = 26.0 bits (58), Expect = 6.1
Identities = 9/31 (29%), Positives = 13/31 (41%)
Query: 112 ITSHGRRDMDRIAAQIRVSKKEAALQALAAQ 142
IT G R Q++V E A+ A +
Sbjct: 17 ITRDGVRVDVTAVFQVKVGGTEEAIATAAER 47
>gnl|CDD|223713 COG0640, ArsR, Predicted transcriptional regulators
[Transcription].
Length = 110
Score = 25.5 bits (55), Expect = 8.0
Identities = 6/61 (9%), Positives = 19/61 (31%), Gaps = 3/61 (4%)
Query: 71 RKRNGVCPSHFCRSSG---SVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQI 127
+ + + G S L+ L + ++E +G ++ + + +
Sbjct: 35 AEGGELTVGELAEALGLSQSTVSHHLKVLREAGLVELRREGRLRLYRLADEKVAELLELL 94
Query: 128 R 128
Sbjct: 95 L 95
>gnl|CDD|178550 PLN02966, PLN02966, cytochrome P450 83A1.
Length = 502
Score = 26.2 bits (57), Expect = 8.0
Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 84 SSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDM 120
SS +A++ L+ + VN ++ G + S+GRRDM
Sbjct: 79 SSAELAKELLK-TQDVNFADRPPHRGHEFISYGRRDM 114
>gnl|CDD|212127 cd10816, GH57N_BE_TK1436_like, N-terminal catalytic domain of Gh57
branching enzyme TK 1436 and similar proteins. The
subfamily is represented by a novel branching-enzyme
TK1436 of hyperthermophilic archaeon Thermococcus
kodakaraensis KOD1. Branching enzymes (BEs, EC 2.4.1.18)
play a key role in synthesis of alpha-glucans and they
generally are classified into glycoside hydrolase family
13 (GH13). However, TK1436 belongs to the GH57 family.
It functions as a monomer and possesses BE activity.
TK1436 is composed of a distorted N-terminal
(beta/alpha)7-barrel domain and a C-terminal five
alpha-helical domain, both of which participate in the
formation of the active-site cleft.
Length = 423
Score = 26.3 bits (58), Expect = 8.9
Identities = 10/26 (38%), Positives = 10/26 (38%)
Query: 27 KSAKFKELAPYDPDWFYTRCAALARH 52
E PYDPD R ARH
Sbjct: 307 PKVDLGEKEPYDPDDAAARVEEHARH 332
>gnl|CDD|181629 PRK09057, PRK09057, coproporphyrinogen III oxidase; Provisional.
Length = 380
Score = 26.0 bits (58), Expect = 9.3
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 69 GGRKRNGVCPSHFCRSSG-SVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQI 127
G R R G+ + + SG + + L L + +IE+ + T GR +D + A +
Sbjct: 319 GLRLREGIDLARYAALSGRPLDPERLADLIEEGLIERDGGSRLRATPAGRLVLDAVVADL 378
>gnl|CDD|224460 COG1543, COG1543, Uncharacterized conserved protein [Function
unknown].
Length = 504
Score = 26.2 bits (58), Expect = 9.5
Identities = 8/24 (33%), Positives = 10/24 (41%), Gaps = 1/24 (4%)
Query: 35 APYDPDWFYTRCAALARH-IYMRS 57
APYDP+ A H + R
Sbjct: 286 APYDPEKAMEAVDEHAAHFVGNRH 309
>gnl|CDD|217060 pfam02481, DNA_processg_A, DNA recombination-mediator protein A.
The SMF family, of DNA processing chain A, dprA, are a
group of bacterial proteins. In H. pylori, dprA is
required for natural chromosomal and plasmid
transformation. It has now been shown that DprA is found
to bind cooperatively to single-stranded DNA (ssDNA) and
to interact with RecA. In the process, DprA-RecA-ssDNA
filaments are produced and these filaments catalyze the
homology-dependent formation of joint molecules. While
the E.coli SSB protein limits access of RecA to ssDNA,
DprA alleviates this barrier. It is proposed that DprA
is a new member of the recombination-mediator protein
family, dedicated to natural bacterial transformation.
Length = 210
Score = 25.5 bits (57), Expect = 9.8
Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 12/44 (27%)
Query: 108 GGRKITSHGRRDMDRIAAQIRVSKKEAALQALAAQGITVVPTGA 151
G RK +++G R ++AA+ LA +GIT+V A
Sbjct: 49 GTRKPSAYGLRVARKLAAE------------LAERGITIVSGLA 80
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
0.320 0.133 0.396
Gapped
Lambda K H
0.267 0.0779 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,841,989
Number of extensions: 710996
Number of successful extensions: 1010
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1005
Number of HSP's successfully gapped: 43
Length of query: 152
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 64
Effective length of database: 7,034,450
Effective search space: 450204800
Effective search space used: 450204800
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 (21.9 bits)
S2: 55 (24.9 bits)