RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9282
(120 letters)
>gnl|CDD|217661 pfam03656, Pam16, Pam16. The Pam16 protein is the fifth essential
subunit of the pre-sequence translocase-associated
protein import motor (PAM). In Saccharomyces cerevisiae,
Pam16 is required for preprotein translocation into the
matrix, but not for protein insertion into the inner
membrane. Pam16 has a degenerate J domain. J-domain
proteins play important regulatory roles as
co-chaperones, recruiting Hsp70 partners and
accelerating the ATP-hydrolysis step of the chaperone
cycle. Pam16's J-like domain strongly interacts with
Pam18's J domain, leading to a productive interaction of
Pam18 with mtHsp70 at the mitochondria import channel.
Pam18 stimulates the ATPase activity of mtHsp70.
Length = 127
Score = 100 bits (250), Expect = 1e-28
Identities = 54/114 (47%), Positives = 77/114 (67%), Gaps = 4/114 (3%)
Query: 1 MAKYI-IQIAVLGAQVVGRAFAKALRQEYAASQEAAKRAGGGRQGTAQASENLRTGMTLD 59
MA IQ+ + G QVVG+AFA+A RQE AA + AA G +++ G++LD
Sbjct: 1 MAHRAAIQVIITGTQVVGKAFARAYRQEAAAQRVAA--GAGTNASRRGTAKSNYGGISLD 58
Query: 60 EARDILDIKQ-LDPKEIKQRYEFLFNANDSSKGGSFYIQSKVVRAKERIDQEVK 112
E+ IL++++ L+ +E+ +RYE LF ND SKGGSFY+QSKV RAKER+D+E+
Sbjct: 59 ESCQILNVEEDLNMEEVNKRYEHLFEVNDKSKGGSFYLQSKVYRAKERLDEELA 112
>gnl|CDD|240265 PTZ00100, PTZ00100, DnaJ chaperone protein; Provisional.
Length = 116
Score = 38.7 bits (90), Expect = 1e-04
Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 56 MTLDEARDILDIKQLDPKE-IKQRYEFLFNANDSSKGGSFYIQSKVVRAKERI 107
M+ EA IL+I KE I++ ++ L N GGS YI SKV AK+ +
Sbjct: 62 MSKSEAYKILNISPTASKERIREAHKQLMLRNHPDNGGSTYIASKVNEAKDLL 114
>gnl|CDD|183033 PRK11197, lldD, L-lactate dehydrogenase; Provisional.
Length = 381
Score = 29.6 bits (67), Expect = 0.37
Identities = 21/69 (30%), Positives = 30/69 (43%), Gaps = 19/69 (27%)
Query: 5 IIQIAVLGAQVV--GRAFAKALRQEYAASQEAAKRAGGGRQGTAQASE----NLRTGMTL 58
++++ LGA V GRAF AL A G+ G A + +R MTL
Sbjct: 315 VVRMIALGADTVLLGRAFVYAL-------------AAAGQAGVANLLDLIEKEMRVAMTL 361
Query: 59 DEARDILDI 67
A+ I +I
Sbjct: 362 TGAKSISEI 370
>gnl|CDD|119328 cd06577, PASTA_pknB, PASTA domain of bacterial serine/threonine
kinase pknB-like proteins. PknB is a member of a group
of related transmembrane sensor kinases present in many
gram positive bacteria, which has been shown to
regulate cell shape in Mycobacterium tubercolosis. PknB
is a receptor-like transmembrane protein with an
extracellular signal sensor domain (containing multiple
PASTA domains) and an intracellular, eukaryotic
serine/threonine kinase-like domain. The PASTA domain
is found at the C-termini of several Penicillin-binding
proteins (PBPs) and bacterial serine/threonine kinases.
The name PASTA is derived from PBP and
Serine/Threonine kinase Associated domain.
Length = 62
Score = 27.1 bits (61), Expect = 0.76
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 54 TGMTLDEARDILDIKQLDPKEIKQRY 79
GMTLDEA+ L+ L + + Y
Sbjct: 6 VGMTLDEAKAALEAAGLKVGVVTEEY 31
>gnl|CDD|224223 COG1304, idi, Isopentenyl diphosphate isomerase (BS_ypgA, MTH48 and
related proteins) [Coenzyme transport and metabolism].
Length = 360
Score = 27.6 bits (62), Expect = 1.4
Identities = 19/65 (29%), Positives = 26/65 (40%), Gaps = 19/65 (29%)
Query: 11 LGAQVV--GRAFAKALRQEYAASQEAAKRAGGGRQGTAQASEN----LRTGMTLDEARDI 64
LGA V GR F L A GG G + E L+ M L A++I
Sbjct: 294 LGADAVGIGRPFLYGL-------------AAGGEAGVERVLEIIRKELKIAMALTGAKNI 340
Query: 65 LDIKQ 69
++K+
Sbjct: 341 EELKR 345
>gnl|CDD|165307 PHA03006, PHA03006, hypothetical protein; Provisional.
Length = 323
Score = 27.7 bits (61), Expect = 1.7
Identities = 16/68 (23%), Positives = 29/68 (42%), Gaps = 2/68 (2%)
Query: 35 AKRAGGGRQGTAQASENLRTGMTLDEARDILDIKQLDPKEIKQRYEFLFNANDSSKGGSF 94
K G + + E + + LD + I D + LD EI++ Y+ + N SF
Sbjct: 187 KKLNGCCEELINKKKEIINFAIKLDISLPIDDFEILDEDEIEEIYDIIENIK--IHKNSF 244
Query: 95 YIQSKVVR 102
I +++
Sbjct: 245 DISMIIIK 252
>gnl|CDD|99804 cd06208, CYPOR_like_FNR, These ferredoxin reductases are related to
the NADPH cytochrome p450 reductases (CYPOR), but lack
the FAD-binding region connecting sub-domain.
Ferredoxin-NADP+ reductase (FNR) is an FAD-containing
enzyme that catalyzes the reversible electron transfer
between NADP(H) and electron carrier proteins, such as
ferredoxin and flavodoxin. Isoforms of these
flavoproteins (i.e. having a non-covalently bound FAD as
a prosthetic group) are present in chloroplasts,
mitochondria, and bacteria in which they participate in
a wide variety of redox metabolic pathways. The
C-terminal domain contains most of the NADP(H) binding
residues and the N-terminal domain interacts
non-covalently with the isoalloxazine rings of the
flavin molecule which lies largely in a large gap
between the two domains. Ferredoxin-NADP+ reductase
first accepts one electron from reduced ferredoxin to
form a flavin semiquinone intermediate. The enzyme then
accepts a second electron to form FADH2, which then
transfers two electrons and a proton to NADP+ to form
NADPH. CYPOR serves as an electron donor in several
oxygenase systems and is a component of nitric oxide
synthases, sulfite reducatase, and methionine synthase
reductases. CYPOR transfers two electrons from NADPH to
the heme of cytochrome p450 via FAD and FMN. CYPOR has
a C-terminal FNR-like FAD and NAD binding module, an
FMN-binding domain, and an additional connecting domain
(inserted within the FAD binding region) that orients
the FNR and FMN -binding domains. The C-terminal domain
contains most of the NADP(H) binding residues, and the
N-terminal domain interacts non-covalently with the
isoalloxazine rings of the flavin molecule, which lies
largely in a large gap betweed the two domains.
Ferredoxin-NADP+ reductase first accepts one electron
from reduced ferredoxin to form a flavin semiquinone
intermediate. The enzyme then accepts a second electron
to form FADH2 which then transfers two electrons and a
proton to NADP+ to form NADPH.
Length = 286
Score = 27.3 bits (61), Expect = 2.1
Identities = 6/21 (28%), Positives = 11/21 (52%)
Query: 87 DSSKGGSFYIQSKVVRAKERI 107
++ GG Y+Q ++ E I
Sbjct: 211 KNADGGKMYVQDRIAEYAEEI 231
>gnl|CDD|226789 COG4339, COG4339, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 208
Score = 26.8 bits (59), Expect = 2.4
Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 8 IAVLGA-QVVGRAFAKALRQEYAASQEAAKRAGGGR 42
+A+L A +V + + A+RQEYA E RAG GR
Sbjct: 134 LAILAANRVDYQEYEHAVRQEYAWVSEPDYRAGRGR 169
>gnl|CDD|221003 pfam11150, DUF2927, Protein of unknown function (DUF2927). This
family is conserved in Proteobacteria. Several members
are described as being putative lipoproteins, but
otherwise the function is not known.
Length = 212
Score = 26.8 bits (60), Expect = 2.5
Identities = 9/14 (64%), Positives = 9/14 (64%)
Query: 52 LRTGMTLDEARDIL 65
LR GMT E R IL
Sbjct: 196 LRPGMTRAEVRPIL 209
>gnl|CDD|166864 PRK00234, PRK00234, Maf-like protein; Reviewed.
Length = 192
Score = 26.6 bits (59), Expect = 3.1
Identities = 13/27 (48%), Positives = 18/27 (66%), Gaps = 2/27 (7%)
Query: 7 QIAVLGAQVVGR--AFAKALRQEYAAS 31
Q+AVLG Q++G+ F +A Q AAS
Sbjct: 70 QVAVLGGQILGKPHTFERAREQLLAAS 96
>gnl|CDD|223166 COG0088, RplD, Ribosomal protein L4 [Translation, ribosomal
structure and biogenesis].
Length = 214
Score = 26.4 bits (59), Expect = 3.1
Identities = 8/34 (23%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 14 QVVGRAFAKALRQEYAASQEAAKRAGGGRQGTAQ 47
+ V A RQ +++ + +GGG++ Q
Sbjct: 35 RAVLAQLANR-RQGTHSTKTRGEVSGGGKKPWGQ 67
>gnl|CDD|222912 PHA02624, PHA02624, large T antigen; Provisional.
Length = 647
Score = 26.9 bits (60), Expect = 3.2
Identities = 11/16 (68%), Positives = 13/16 (81%)
Query: 96 IQSKVVRAKERIDQEV 111
IQ KVV KER+D+EV
Sbjct: 604 IQEKVVTWKERLDKEV 619
>gnl|CDD|223024 PHA03252, PHA03252, DNA packaging tegument protein UL25;
Provisional.
Length = 589
Score = 26.6 bits (59), Expect = 3.5
Identities = 12/46 (26%), Positives = 14/46 (30%)
Query: 27 EYAASQEAAKRAGGGRQGTAQASENLRTGMTLDEARDILDIKQLDP 72
E G R AQ+ E G E + I Q DP
Sbjct: 99 GATNGGEVNVDGGADRTWLAQSPERPADGGPSGERVNQFGITQNDP 144
>gnl|CDD|238101 cd00172, SERPIN, SERine Proteinase INhibitors (serpins) exhibit
conformational polymorphism shifting from native to
cleaved, latent, delta, or polymorphic forms. Many
serpins, such as antitrypsin and antichymotrypsin,
function as serine protease inhibitors which regulate
blood coagulation cascades. Non-inhibitory serpins
perform many diverse functions such as chaperoning
proteins or transporting hormones. Serpins are of
medical interest because mutants have been associated
with blood clotting disorders, emphysema, cirrhosis, and
dementia.
Length = 364
Score = 26.4 bits (59), Expect = 4.5
Identities = 12/48 (25%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 54 TGMTLDEARDILDIKQLDPKEIKQRYEFLFNA-NDSSKGGSFYIQSKV 100
G T ++ R +L + LD +++ Q ++ L ++ DS KG + +++
Sbjct: 41 GGETREQLRKVLGLPSLDDEDVHQAFKSLLSSLKDSEKGVELKLANRL 88
>gnl|CDD|133384 cd01109, HTH_YyaN, Helix-Turn-Helix DNA binding domain of the
MerR-like transcription regulators YyaN and YraB.
Putative helix-turn-helix (HTH) MerR-like transcription
regulators of Bacillus subtilis, YyaN and YraB, and
related proteins; N-terminal domain. Based on sequence
similarity, these proteins are predicted to function as
transcription regulators that mediate responses to
stress in eubacteria. They belong to the MerR
superfamily of transcription regulators that promote
transcription of various stress regulons by
reconfiguring the operator sequence located between the
-35 and -10 promoter elements. A typical MerR regulator
is comprised of distinct domains that harbor the
regulatory (effector-binding) site and the active
(DNA-binding) site. Their N-terminal domains are
homologous and contain a DNA-binding winged HTH motif,
while the C-terminal domains are often dissimilar and
bind specific coactivator molecules such as metal ions,
drugs, and organic substrates.
Length = 113
Score = 25.1 bits (56), Expect = 6.1
Identities = 7/29 (24%), Positives = 17/29 (58%)
Query: 54 TGMTLDEARDILDIKQLDPKEIKQRYEFL 82
TGM++ + ++ ++++ I +R E L
Sbjct: 56 TGMSIKDIKEYAELRREGDSTIPERLELL 84
>gnl|CDD|181057 PRK07608, PRK07608, ubiquinone biosynthesis hydroxylase family
protein; Provisional.
Length = 388
Score = 25.7 bits (57), Expect = 6.4
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 7 QIAVLGAQVVGRAFAKALRQ 26
+ V+G +VG + A AL Q
Sbjct: 7 DVVVVGGGLVGASLALALAQ 26
>gnl|CDD|234709 PRK00275, glnD, PII uridylyl-transferase; Provisional.
Length = 895
Score = 25.8 bits (57), Expect = 6.7
Identities = 19/57 (33%), Positives = 26/57 (45%), Gaps = 5/57 (8%)
Query: 21 AKALRQEYAASQEAAKRAGGGRQGTAQASENLRTGMTLDEARDILDIKQLDPKEIKQ 77
A LRQ Y ++ A +R G + E +R T A DIL K DP + +Q
Sbjct: 604 ASLLRQLYTETKRALRR---GLENPVDREEQIRQ--TQSAALDILVRKGTDPDDAEQ 655
>gnl|CDD|233062 TIGR00630, uvra, excinuclease ABC, A subunit. This family is a
member of the ABC transporter superfamily of proteins of
which all members for which functions are known except
the UvrA proteins are involved in the transport of
material through membranes. UvrA orthologs are involved
in the recognition of DNA damage as a step in nucleotide
excision repair. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 925
Score = 25.7 bits (57), Expect = 7.8
Identities = 10/41 (24%), Positives = 19/41 (46%), Gaps = 10/41 (24%)
Query: 54 TGMTLDEARDILDIKQLDP----------KEIKQRYEFLFN 84
+ +++ EA + + L P KEI++R FL +
Sbjct: 434 SELSIREAHEFFNQLTLTPEEKKIAEEVLKEIRERLGFLID 474
>gnl|CDD|237054 PRK12316, PRK12316, peptide synthase; Provisional.
Length = 5163
Score = 25.7 bits (56), Expect = 8.2
Identities = 12/38 (31%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 51 NLRTGMTLDEARDILDIKQLDPKEIKQRYEFLFNANDS 88
NL M D R + +++ L+ E +QR L+N D+
Sbjct: 4509 NLLEAMAEDPQRRLGELQLLEKAE-QQRIVALWNRTDA 4545
>gnl|CDD|233216 TIGR00970, leuA_yeast, 2-isopropylmalate synthase, yeast type. A
larger family of homologous proteins includes
homocitrate synthase, distinct lineages of
2-isopropylmalate synthase, several distinct,
uncharacterized, orthologous sets in the Archaea, and
other related enzymes. This model describes a family of
2-isopropylmalate synthases as found in yeasts and in a
minority of studied bacteria [Amino acid biosynthesis,
Pyruvate family].
Length = 564
Score = 25.6 bits (56), Expect = 9.2
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 70 LDPKEIKQRYEFLFNANDSS-KGGSFYI 96
LDP+++ + YE + N S KGG YI
Sbjct: 366 LDPRDVGRTYEAVIRVNSQSGKGGVAYI 393
>gnl|CDD|239203 cd02809, alpha_hydroxyacid_oxid_FMN, Family of homologous
FMN-dependent alpha-hydroxyacid oxidizing enzymes. This
family occurs in both prokaryotes and eukaryotes.
Members of this family include flavocytochrome b2
(FCB2), glycolate oxidase (GOX), lactate monooxygenase
(LMO), mandelate dehydrogenase (MDH), and long chain
hydroxyacid oxidase (LCHAO). In green plants, glycolate
oxidase is one of the key enzymes in photorespiration
where it oxidizes glycolate to glyoxylate. LMO catalyzes
the oxidation of L-lactate to acetate and carbon
dioxide. MDH oxidizes (S)-mandelate to phenylglyoxalate.
It is an enzyme in the mandelate pathway that occurs in
several strains of Pseudomonas which converts
(R)-mandelate to benzoate.
Length = 299
Score = 25.5 bits (57), Expect = 9.3
Identities = 17/65 (26%), Positives = 20/65 (30%), Gaps = 19/65 (29%)
Query: 11 LGAQVV--GRAFAKALRQEYAASQEAAKRAGGGRQGTAQA----SENLRTGMTLDEARDI 64
LGA V GR F L A GG G A + L M L +
Sbjct: 248 LGADAVLIGRPFLYGL-------------AAGGEAGVAHVLEILRDELERAMALLGCASL 294
Query: 65 LDIKQ 69
D+
Sbjct: 295 ADLDP 299
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
0.314 0.129 0.340
Gapped
Lambda K H
0.267 0.0769 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,085,675
Number of extensions: 537562
Number of successful extensions: 691
Number of sequences better than 10.0: 1
Number of HSP's gapped: 689
Number of HSP's successfully gapped: 50
Length of query: 120
Length of database: 10,937,602
Length adjustment: 83
Effective length of query: 37
Effective length of database: 7,256,220
Effective search space: 268480140
Effective search space used: 268480140
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 53 (24.1 bits)