RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2143
(149 letters)
>gnl|CDD|185442 PTZ00096, PTZ00096, 40S ribosomal protein S15; Provisional.
Length = 143
Score = 180 bits (460), Expect = 1e-59
Identities = 74/105 (70%), Positives = 85/105 (80%)
Query: 45 ETQKKKRTFRKFTFRGVDLDQLLDMPTEQLMELMHCRARRRFARGIKRKPMALVKKLRKA 104
E KKKRTF+KFT+RGV+L++LL +P E+L+EL R RRR RGIKRK L+KKLRKA
Sbjct: 4 EQLKKKRTFKKFTYRGVELEKLLALPEEELVELFRARQRRRINRGIKRKHPTLLKKLRKA 63
Query: 105 KKEAPPNEKPEVVKTHLRNMIIVPEMVGSVVGVYNGKTFNQVEIK 149
KK P EKP+ VKTHLR+MIIVPEMVGSVVGVYNGK FN VEIK
Sbjct: 64 KKATKPGEKPKAVKTHLRDMIIVPEMVGSVVGVYNGKQFNNVEIK 108
>gnl|CDD|130097 TIGR01025, rpsS_arch, ribosomal protein
S19(archaeal)/S15(eukaryotic). This model represents
eukaryotic ribosomal protein S15 and its archaeal
equivalent. It excludes bacterial and organellar
ribosomal protein S19. The nomenclature for the archaeal
members is unresolved and given variously as S19 (after
the more distant bacterial homologs) or S15 [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 135
Score = 141 bits (358), Expect = 2e-44
Identities = 61/98 (62%), Positives = 75/98 (76%)
Query: 52 TFRKFTFRGVDLDQLLDMPTEQLMELMHCRARRRFARGIKRKPMALVKKLRKAKKEAPPN 111
TF++F +RG L++L DM E+L +L+ R RRR RG+ K L+KKLRKAKKEAP
Sbjct: 1 TFKEFRYRGYTLEELQDMSLEELAKLLPARQRRRLKRGLTPKQKKLLKKLRKAKKEAPKG 60
Query: 112 EKPEVVKTHLRNMIIVPEMVGSVVGVYNGKTFNQVEIK 149
EKPEV++TH R+MII+PEMVGS VGVYNGK F QVEIK
Sbjct: 61 EKPEVIRTHCRDMIILPEMVGSTVGVYNGKEFVQVEIK 98
>gnl|CDD|235209 PRK04038, rps19p, 30S ribosomal protein S19P; Provisional.
Length = 134
Score = 109 bits (275), Expect = 1e-31
Identities = 43/96 (44%), Positives = 66/96 (68%), Gaps = 3/96 (3%)
Query: 54 RKFTFRGVDLDQLLDMPTEQLMELMHCRARRRFARGIKRKPMALVKKLRKAKKEAPPNEK 113
++FT+RG L++L +M E+ EL+ R RR RG+ + L++K+RKA++E +K
Sbjct: 5 KEFTYRGYTLEELQEMSLEEFAELLPARQRRSLKRGLTPEQRKLLEKIRKARREK---KK 61
Query: 114 PEVVKTHLRNMIIVPEMVGSVVGVYNGKTFNQVEIK 149
V++TH+R+MII+PEMVG + VYNGK F +VEI
Sbjct: 62 GRVIRTHVRDMIILPEMVGLTIAVYNGKEFVEVEIV 97
>gnl|CDD|201079 pfam00203, Ribosomal_S19, Ribosomal protein S19.
Length = 81
Score = 93.2 bits (232), Expect = 6e-26
Identities = 32/62 (51%), Positives = 38/62 (61%), Gaps = 1/62 (1%)
Query: 88 RGIKRKPMALVKKLRKAKKEAPPNEKPEVVKTHLRNMIIVPEMVGSVVGVYNGKTFNQVE 147
R +K+ P +K LRK KKE NEK EV+KT R I+PEMVG + VYNGK F V
Sbjct: 1 RSLKKGPFVDLKLLRKIKKENTKNEK-EVIKTWSRRSTILPEMVGHTIAVYNGKEFVPVY 59
Query: 148 IK 149
I
Sbjct: 60 IT 61
>gnl|CDD|223263 COG0185, RpsS, Ribosomal protein S19 [Translation, ribosomal
structure and biogenesis].
Length = 93
Score = 72.6 bits (179), Expect = 9e-18
Identities = 28/66 (42%), Positives = 38/66 (57%), Gaps = 7/66 (10%)
Query: 87 ARGIKRKPMA---LVKKLRKAKKEAPPNEKPEVVKTHLRNMIIVPEMVGSVVGVYNGKTF 143
R +K+ P L+KK+RKAK+ K + +KT R I+PEMVG + V+NGK F
Sbjct: 2 RRSLKKGPFVDKHLLKKVRKAKES----GKKKPIKTWSRRSTILPEMVGLTIAVHNGKKF 57
Query: 144 NQVEIK 149
VEI
Sbjct: 58 VPVEIT 63
>gnl|CDD|178985 PRK00357, rpsS, 30S ribosomal protein S19; Reviewed.
Length = 92
Score = 45.6 bits (109), Expect = 3e-07
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 7/65 (10%)
Query: 87 ARGIKRKPMA---LVKKLRKAKKEAPPNEKPEVVKTHLRNMIIVPEMVGSVVGVYNGKTF 143
AR +K+ P L+KK+ KA + + +V+KT R I+PE VG + V+NG+
Sbjct: 2 ARSLKKGPFVDGHLLKKVEKANE----SGDKKVIKTWSRRSTILPEFVGLTIAVHNGRKH 57
Query: 144 NQVEI 148
V +
Sbjct: 58 VPVYV 62
>gnl|CDD|130122 TIGR01050, rpsS_bact, ribosomal protein S19, bacterial/organelle.
The homologous protein of the eukaryotic cytosol and of
the Archaea may be designated S15 or S19 [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 92
Score = 42.3 bits (100), Expect = 4e-06
Identities = 24/66 (36%), Positives = 36/66 (54%), Gaps = 7/66 (10%)
Query: 87 ARGIKRKPMA---LVKKLRKAKKEAPPNEKPEVVKTHLRNMIIVPEMVGSVVGVYNGKTF 143
+R +K+ P L+KK+ K + K +V+KT R I+PEM+G + V+NGK F
Sbjct: 2 SRSLKKGPFVDHHLLKKVEKLNES----GKKKVIKTWSRRSTIIPEMIGHTIAVHNGKKF 57
Query: 144 NQVEIK 149
V I
Sbjct: 58 IPVYIT 63
>gnl|CDD|176991 CHL00050, rps19, ribosomal protein S19.
Length = 92
Score = 39.9 bits (94), Expect = 3e-05
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 87 ARGIKRKPMALVKKLRKAKKEAPPNEKPEVVKTHLRNMIIVPEMVGSVVGVYNGKTF 143
R +K+ P L+K +K EK E++ T R I+P M+G + V+NGK
Sbjct: 2 TRSLKKNPFVANHLLKKIEKLNTKEEK-EIIVTWSRASTIIPTMIGHTIAVHNGKEH 57
>gnl|CDD|216071 pfam00704, Glyco_hydro_18, Glycosyl hydrolases family 18.
Length = 325
Score = 30.9 bits (70), Expect = 0.21
Identities = 11/40 (27%), Positives = 19/40 (47%), Gaps = 8/40 (20%)
Query: 33 GEYRTRNFSTVEETQKKKRTF--------RKFTFRGVDLD 64
G + FS + K++TF +K+ F G+D+D
Sbjct: 80 GWTFSGGFSLLASDDAKRKTFADSIIDFLKKYGFDGIDID 119
>gnl|CDD|214753 smart00636, Glyco_18, Glyco_18 domain.
Length = 334
Score = 29.2 bits (66), Expect = 0.66
Identities = 10/40 (25%), Positives = 19/40 (47%), Gaps = 8/40 (20%)
Query: 33 GEYRTRNFSTVEETQKKKRTF--------RKFTFRGVDLD 64
G + NFS++ ++ F +K+ F G+D+D
Sbjct: 75 GWTESDNFSSMLSDPASRKKFIDSIVSFLKKYGFDGIDID 114
>gnl|CDD|119365 cd06548, GH18_chitinase, The GH18 (glycosyl hydrolases, family 18)
type II chitinases hydrolyze chitin, an abundant polymer
of N-acetylglucosamine and have been identified in
bacteria, fungi, insects, plants, viruses, and protozoan
parasites. The structure of this domain is an
eight-stranded alpha/beta barrel with a pronounced
active-site cleft at the C-terminal end of the
beta-barrel.
Length = 322
Score = 29.1 bits (66), Expect = 0.78
Identities = 10/35 (28%), Positives = 15/35 (42%), Gaps = 8/35 (22%)
Query: 38 RNFSTVEETQKKKRTF--------RKFTFRGVDLD 64
FS T+ + F RK+ F G+D+D
Sbjct: 98 GGFSDAAATEASRAKFADSAVDFIRKYGFDGIDID 132
>gnl|CDD|220096 pfam09052, SipA, Salmonella invasion protein A. Salmonella
invasion protein A is an actin-binding protein that
contributes to host cytoskeletal rearrangements by
stimulating actin polymerisation and counteracting
F-actin destabilising proteins. Members of this family
possess an all-helical fold consisting of eight
alpha-helices arranged so that six long, amphipathic
helices form a compact fold that surrounds a final,
predominantly hydrophobic helix in the middle of the
molecule.
Length = 674
Score = 29.2 bits (65), Expect = 0.99
Identities = 15/83 (18%), Positives = 32/83 (38%), Gaps = 9/83 (10%)
Query: 47 QKKKRTFRKFTFRGVDLDQLLDMPTEQLMELMHCRARRRFARGIKR-------KPMALVK 99
K F F FR + D L PT + + A ++ ++ KP +
Sbjct: 501 TDSKGLFTGFFFR--NGDTYLTRPTIAYLRGLAFEASKKVLNSLRNALEPIGTKPGTQRR 558
Query: 100 KLRKAKKEAPPNEKPEVVKTHLR 122
+ ++ +K+ P++ + L+
Sbjct: 559 EFQELRKDILPSDTEHRINNKLK 581
>gnl|CDD|233816 TIGR02302, aProt_lowcomp, TIGR02302 family protein. Members of
this family are long (~850 residue) bacterial proteins
from the alpha Proteobacteria. Each has 2-3 predicted
transmembrane helices near the N-terminus and a long
C-terminal region that includes stretches of
Gln/Gly-rich low complexity sequence, predicted by TMHMM
to be outside the membrane. In Bradyrhizobium japonicum,
two tandem reading frames are together homologous the
single members found in other species; the cutoffs
scores are set low enough that the longer scores above
the trusted cutoff and the shorter above the noise
cutoff for this model.
Length = 851
Score = 28.4 bits (63), Expect = 1.6
Identities = 19/87 (21%), Positives = 33/87 (37%), Gaps = 10/87 (11%)
Query: 30 NDRGEYRTRNFSTVEETQKKKRTFRKFTFRGVDLDQLL--DMPTE--------QLMELMH 79
N GE + +ET K + R+ RG D +Q DMP + L + +
Sbjct: 626 NKLGELMRKQQQLRDETFKLDQDQRRDRMRGQDGEQNFGDDMPQQDGQPNGQPNLHDRLR 685
Query: 80 CRARRRFARGIKRKPMALVKKLRKAKK 106
+ RG+ + L +L + +
Sbjct: 686 KLQQEEAKRGLGQSQGGLKGELGQLGQ 712
>gnl|CDD|220419 pfam09814, DUF2351, Uncharacterized conserved protein (DUF2351).
Members of this family of proteins have no known
function.
Length = 350
Score = 28.3 bits (63), Expect = 1.6
Identities = 10/24 (41%), Positives = 15/24 (62%), Gaps = 3/24 (12%)
Query: 60 GVDLDQLLDMPTEQLMELM---HC 80
+ D++LD+P+E ELM HC
Sbjct: 119 SRNFDRVLDLPSENWAELMDFWHC 142
>gnl|CDD|201673 pfam01229, Glyco_hydro_39, Glycosyl hydrolases family 39.
Length = 486
Score = 27.5 bits (61), Expect = 3.4
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 3/58 (5%)
Query: 85 RFARGIKRKPMALVKKLRKAKKEAPPNEKPEVVKTH---LRNMIIVPEMVGSVVGVYN 139
RF G R +AL ++L A K A P+ E ++ H ++I E G + YN
Sbjct: 25 RFCVGADRYDLALDQQLNLALKGAVPHLGFEYIRFHGLLNDDLITARESNGDGLLSYN 82
>gnl|CDD|119351 cd02872, GH18_chitolectin_chitotriosidase, This conserved domain
family includes a large number of catalytically inactive
chitinase-like lectins (chitolectins) including YKL-39,
YKL-40 (HCGP39), YM1, oviductin, and AMCase (acidic
mammalian chitinase), as well as catalytically active
chitotriosidases. The conserved domain is an
eight-stranded alpha/beta barrel fold belonging to the
family 18 glycosyl hydrolases. The fold has a
pronounced active-site cleft at the C-terminal end of
the beta-barrel. The chitolectins lack a key active
site glutamate (the proton donor required for hydrolytic
activity) but retain highly conserved residues involved
in oligosaccharide binding. Chitotriosidase is a
chitinolytic enzyme expressed in maturing macrophages,
which suggests that it plays a part in antimicrobial
defense. Chitotriosidase hydrolyzes chitotriose, as
well as colloidal chitin to yield chitobiose and is
therefore considered an exochitinase. Chitotriosidase
occurs in two major forms, the large form being
converted to the small form by either RNA or
post-translational processing. Although the small form,
containing the chitinase domain alone, is sufficient for
the chitinolytic activity, the additional C-terminal
chitin-binding domain of the large form plays a role in
processing colloidal chitin. The chitotriosidase gene is
nonessential in humans, as about 35% of the population
are heterozygous and 6% homozygous for an inactivated
form of the gene. HCGP39 is a 39-kDa human cartilage
glycoprotein thought to play a role in connective tissue
remodeling and defense against pathogens.
Length = 362
Score = 27.1 bits (61), Expect = 3.7
Identities = 22/88 (25%), Positives = 36/88 (40%), Gaps = 32/88 (36%)
Query: 37 TRNFSTVEETQKKKRTF--------RKFTFRGVDLD-----QLLDMPTEQLMELMHCRAR 83
+ FS + + + ++TF RK+ F G+DLD Q P + +
Sbjct: 84 SAKFSAMAASPENRKTFIKSAIAFLRKYGFDGLDLDWEYPGQRGGPPED----------K 133
Query: 84 RRFARGIKRKPMALVKKLRKA-KKEAPP 110
F L+K+LR+A + EAP
Sbjct: 134 ENFVT--------LLKELREAFEPEAPR 153
>gnl|CDD|225862 COG3325, ChiA, Chitinase [Carbohydrate transport and metabolism].
Length = 441
Score = 27.0 bits (60), Expect = 4.0
Identities = 8/36 (22%), Positives = 12/36 (33%), Gaps = 8/36 (22%)
Query: 37 TRNFSTVEETQKK--------KRTFRKFTFRGVDLD 64
+ FS + R + F GVD+D
Sbjct: 139 SGGFSDMAADDASRENFAKSAVEFMRTYGFDGVDID 174
>gnl|CDD|182449 PRK10425, PRK10425, DNase TatD; Provisional.
Length = 258
Score = 26.9 bits (60), Expect = 4.3
Identities = 21/55 (38%), Positives = 23/55 (41%), Gaps = 23/55 (41%)
Query: 38 RNFSTVEETQKKKRTFRKFTFRGVDLDQL-----LDMPTEQLMELMHCR-ARRRF 86
RNFST EE + R F QL L+MP MHCR A RF
Sbjct: 98 RNFSTPEEQE------RAFV------AQLAIAAELNMPV-----FMHCRDAHERF 135
>gnl|CDD|215625 PLN03192, PLN03192, Voltage-dependent potassium channel;
Provisional.
Length = 823
Score = 27.1 bits (60), Expect = 4.7
Identities = 13/26 (50%), Positives = 15/26 (57%)
Query: 56 FTFRGVDLDQLLDMPTEQLMELMHCR 81
FTFR L QLL + T L+E M R
Sbjct: 461 FTFRTKTLSQLLRLKTSTLIEAMQTR 486
>gnl|CDD|222208 pfam13537, GATase_7, Glutamine amidotransferase domain. This
domain is a class-II glutamine amidotransferase domain
found in a variety of enzymes such as asparagine
synthetase and glutamine-fructose-6-phosphate
transaminase.
Length = 120
Score = 25.9 bits (58), Expect = 4.9
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 8/38 (21%)
Query: 120 HLRNMIIVPE-----MV---GSVVGVYNGKTFNQVEIK 149
H R I E MV G V V+NG+ +N E++
Sbjct: 1 HRRLSIDDSEGGAQPMVSEDGRYVIVFNGEIYNYRELR 38
>gnl|CDD|237377 PRK13405, bchH, magnesium chelatase subunit H; Provisional.
Length = 1209
Score = 26.9 bits (60), Expect = 5.1
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 89 GIKRKPMALVKKLRKAKKEAPPN 111
G P+AL+KKLR KKE +
Sbjct: 122 GPASGPLALLKKLRGKKKEGGSS 144
>gnl|CDD|217145 pfam02616, ScpA_ScpB, ScpA/B protein. ScpA and ScpB participate in
chromosomal partition during cell division. It may act
via the formation of a condensin-like complex containing
smc that pull DNA away from mid-cell into both cell
halves. These proteins are part of the Kleisin
superfamily.
Length = 177
Score = 26.6 bits (59), Expect = 5.3
Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 2/71 (2%)
Query: 47 QKKKRTFRKFTFRGVDLDQLLDMPTEQLMELMHCRARR--RFARGIKRKPMALVKKLRKA 104
K + R F+ + V LD+ + E+L+E+ F + +KRK ++K +
Sbjct: 49 MKAEALLRSFSKKPVTLDEFIKTLEEELVEVEKSVLDLIHAFNKLVKRKRKNRLRKKNET 108
Query: 105 KKEAPPNEKPE 115
+ E E E
Sbjct: 109 ELEVSVEEVLE 119
>gnl|CDD|225181 COG2272, PnbA, Carboxylesterase type B [Lipid metabolism].
Length = 491
Score = 26.6 bits (59), Expect = 6.2
Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 1/46 (2%)
Query: 42 TVEETQKKKRTF-RKFTFRGVDLDQLLDMPTEQLMELMHCRARRRF 86
+ EE ++K F R LD+L + E L++ R F
Sbjct: 222 SREEAREKAAAFARALGIPEATLDKLRALSAEDLVKARLPLIGRTF 267
>gnl|CDD|215611 PLN03167, PLN03167, Chaperonin-60 beta subunit; Provisional.
Length = 600
Score = 26.8 bits (59), Expect = 6.2
Identities = 16/50 (32%), Positives = 24/50 (48%)
Query: 87 ARGIKRKPMALVKKLRKAKKEAPPNEKPEVVKTHLRNMIIVPEMVGSVVG 136
RGI++ ALVK+L+K KE +E +V N V M+ +
Sbjct: 172 TRGIEKTAKALVKELKKMSKEVEDSELADVAAVSAGNNYEVGNMIAEAMS 221
>gnl|CDD|111047 pfam02108, FliH, Flagellar assembly protein FliH.
Length = 128
Score = 25.6 bits (57), Expect = 8.2
Identities = 15/73 (20%), Positives = 33/73 (45%)
Query: 63 LDQLLDMPTEQLMELMHCRARRRFARGIKRKPMALVKKLRKAKKEAPPNEKPEVVKTHLR 122
L +L +QL++L AR+ R + P ++ +R+A P ++ +
Sbjct: 18 LAELDQELEQQLVDLALDIARQVIRRELTVDPELILALVREALAALPVLSGKVTLRLNPD 77
Query: 123 NMIIVPEMVGSVV 135
++ +V E +G +
Sbjct: 78 DLALVEEHLGDEL 90
>gnl|CDD|226338 COG3817, COG3817, Predicted membrane protein [Function unknown].
Length = 313
Score = 26.3 bits (58), Expect = 8.3
Identities = 8/52 (15%), Positives = 20/52 (38%)
Query: 95 MALVKKLRKAKKEAPPNEKPEVVKTHLRNMIIVPEMVGSVVGVYNGKTFNQV 146
+A +++ E+ E L N + +P ++ V+ + F +
Sbjct: 67 IAGFGQVKIGALPELSPEEREKSANRLGNRLFIPALLIPVLTLIGSLLFPDL 118
>gnl|CDD|176179 cd05195, enoyl_red, enoyl reductase of polyketide synthase.
Putative enoyl reductase of polyketide synthase.
Polyketide synthases produce polyketides in step by step
mechanism that is similar to fatty acid synthesis. Enoyl
reductase reduces a double to single bond. Erythromycin
is one example of a polyketide generated by 3 complex
enzymes (megasynthases). 2-enoyl thioester reductase
(ETR) catalyzes the NADPH-dependent dependent conversion
of trans-2-enoyl acyl carrier protein/coenzyme A
(ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis.
2-enoyl thioester reductase activity has been linked in
Candida tropicalis as essential in maintaining
mitiochondrial respiratory function. This ETR family is
a part of the medium chain dehydrogenase/reductase
family, but lack the zinc coordination sites
characteristic of the alcohol dehydrogenases in this
family. NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes or ketones. Alcohol dehydrogenase in the liver
converts ethanol and NAD+ to acetaldehyde and NADH,
while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and have 2 tightly bound
zinc atoms per subunit, a catalytic zinc at the active
site, and a structural zinc in a lobe of the catalytic
domain. NAD(H) binding occurs in the cleft between the
catalytic and coenzyme-binding domains, at the active
site, and coenzyme binding induces a conformational
closing of this cleft. Coenzyme binding typically
precedes and contributes to substrate binding.
Length = 293
Score = 26.0 bits (58), Expect = 9.4
Identities = 12/34 (35%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 57 TFRGVDLDQLLDMPTEQLMELMHCRARRRFARGI 90
+F VDLDQL E L EL+ G+
Sbjct: 229 SFSSVDLDQLARERPELLRELLR-EVLELLEAGV 261
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 0.133 0.375
Gapped
Lambda K H
0.267 0.0902 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,460,228
Number of extensions: 680811
Number of successful extensions: 791
Number of sequences better than 10.0: 1
Number of HSP's gapped: 786
Number of HSP's successfully gapped: 36
Length of query: 149
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 61
Effective length of database: 7,034,450
Effective search space: 429101450
Effective search space used: 429101450
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: 54 (24.3 bits)