RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10370
(280 letters)
>gnl|CDD|225758 COG3217, COG3217, Uncharacterized Fe-S protein [General function
prediction only].
Length = 270
Score = 112 bits (281), Expect = 2e-29
Identities = 75/271 (27%), Positives = 119/271 (43%), Gaps = 44/271 (16%)
Query: 9 DRSFVLFNEKEKNFISSKKFNHLLLIQTEYMGGGAFQFSVYNQPSYEKLTIQVADILQTS 68
DR F+L + + FI++++ ++ Y G P E+L ++ AD
Sbjct: 33 DRRFMLVDP-DGRFITARRRPAMVRFTPAYEHDGLR----LTAPDGEELYVRFAD----- 82
Query: 69 HTKSFTLYVDEVLEAFDCGDLASDWFAKYLLNQSDRSIRLGLSTNRRRSIGDNYLRKYTT 128
++ + A GD A+DW + +L R++ L R G + R
Sbjct: 83 AQRAPVEVWGDHFTADAAGDAANDWLSGFL----GRAVSL-------RWDGAGFAR---- 127
Query: 129 VYDNVNDEDIGV---YADMTSYMVLNENSLRDLNKKMSDIGVEDVSMLQFRGNIVVDGPP 185
V +AD ++ N SL DL +++ ++ M +FR N+VV+G
Sbjct: 128 ----RVKAGPAVPVTFADGYPILLFNTASLADLRRRVP----ANLEMERFRPNLVVEGED 179
Query: 186 SYAEDTWDWVRFNSDVITRQVKPCTRCILTTVHPDTGRKQPDSQPLKMLQMYRAVPDLER 245
++AED+W +R V VKPC+RCI TTV PDTG ++P +PL L +R PD
Sbjct: 180 AFAEDSWKSIRI-GGVRFDVVKPCSRCIFTTVDPDTGERRPGGEPLFTLNRFRTNPD--- 235
Query: 246 RKVENFAPMFGVYMGVHRTGYVNVGDDVYVG 276
+FG + G + VGD V V
Sbjct: 236 ----AGGVLFGQNLIARNEGRIRVGDAVEVL 262
>gnl|CDD|215384 PLN02724, PLN02724, Molybdenum cofactor sulfurase.
Length = 805
Score = 73.0 bits (179), Expect = 2e-14
Identities = 61/280 (21%), Positives = 111/280 (39%), Gaps = 25/280 (8%)
Query: 2 VQDGCLEDRSFVLFNEKEKNFISSKKFNHLLLIQTEYMGGGAFQFSVYNQPSYEKLTIQV 61
+ G L DR +++ ++ KK + LI T ++ + + V KL I +
Sbjct: 542 SETGLLYDREWMI-QSLTGEILTQKKVPEMCLITT-FIDLESGKLVVRAPRCDHKLEIPL 599
Query: 62 ADILQTSHTKSFTLYVDEVLEAFDCGDLASDWFAKYLLNQSDRSIRLGLSTNRRRSIGDN 121
Q + L + E+ G ++WF LG R N
Sbjct: 600 ESDSQHEESGEVILCGNRA-ESMSYGTEINEWFTN----------ALGRRCTLVRKSSSN 648
Query: 122 Y---LRKYTTVYDNVNDEDIGVYADMTSYMVLNENSLRDLNKKMS---DIGVEDVSMLQF 175
+ + +DE +A+ +++++E S+ DLN++++ + + +F
Sbjct: 649 TRVCRNRNPSHSPCGDDESRLSFANEGQFLLISEASVEDLNRRLATGQEDAKIRLDPTRF 708
Query: 176 RGNIVVDGPPSYAEDTWDWVRFNSDVITRQVKPCTRCILTTVHPDTGRKQPDSQPLKMLQ 235
R N+VV G +YAED W + T + C RC + + +TG P ++PL L
Sbjct: 709 RPNLVVSGGEAYAEDEWQSLSIGDAEFT-VLGGCNRCQMINIDQETGLVNPSNEPLATLA 767
Query: 236 MYRAVPDLERRKVENFAPMFGVYMGVHRTGYVNVGDDVYV 275
YR V + K+ F + + R ++ VG V
Sbjct: 768 SYRRV----KGKI-LFGILLRYEISDKRDQWIAVGSRVNP 802
>gnl|CDD|217583 pfam03473, MOSC, MOSC domain. The MOSC (MOCO sulfurase C-terminal)
domain is a superfamily of beta-strand-rich domains
identified in the molybdenum cofactor sulfurase and
several other proteins from both prokaryotes and
eukaryotes. These MOSC domains contain an absolutely
conserved cysteine and occur either as stand-alone
forms, or fused to other domains such as NifS-like
catalytic domain in Molybdenum cofactor sulfurase. The
MOSC domain is predicted to be a sulfur-carrier domain
that receives sulfur abstracted by the pyridoxal
phosphate-dependent NifS-like enzymes, on its conserved
cysteine, and delivers it for the formation of diverse
sulfur-metal clusters.
Length = 124
Score = 60.5 bits (147), Expect = 1e-11
Identities = 35/129 (27%), Positives = 52/129 (40%), Gaps = 29/129 (22%)
Query: 149 VLNENSLRDLNKKMSDIGVEDVSMLQFRGNIVVDGPPSYAEDTWDWVR--FNSDVITRQV 206
+++ SL DLN ++ G+ + +FR N+VV G EDTW V+
Sbjct: 23 LISRESLADLNARL---GLRLLDPGRFRENLVVSGLE---EDTWCIGDRIRIGGVLLEVS 76
Query: 207 KPCTRCILTTVHPDTGRKQPDSQPLKMLQMYRAVPDLERRKVENFAPMFGVYMGVHRTGY 266
PC C++ V +TG ER A G+Y V R G
Sbjct: 77 GPCKPCVMLCVDQETG---------------------ERVGRYLAAGKRGIYARVLRPGT 115
Query: 267 VNVGDDVYV 275
+ VGD+V +
Sbjct: 116 IRVGDEVEL 124
>gnl|CDD|217584 pfam03476, MOSC_N, MOSC N-terminal beta barrel domain. This domain
is found to the N-terminus of pfam03473. The function of
this domain is unknown, however it is predicted to adopt
a beta barrel fold.
Length = 118
Score = 45.4 bits (108), Expect = 2e-06
Identities = 23/94 (24%), Positives = 40/94 (42%), Gaps = 7/94 (7%)
Query: 5 GCLEDRSFVLFNEKEKNFISSKKFNHLLLIQTEYMGGGAFQFSVYNQPSYEKLTIQVADI 64
G DR +++ + K FI++++ L+LI+T G + P L++ +
Sbjct: 29 GLRWDRRWMVVDSDGK-FITARRHPRLVLIRTTLDEDGGLTLTA---PGMPPLSV---PL 81
Query: 65 LQTSHTKSFTLYVDEVLEAFDCGDLASDWFAKYL 98
L DCGD A+DWF+ +L
Sbjct: 82 AANKFQLVGVLVWGLSFSGRDCGDAAADWFSDFL 115
>gnl|CDD|188602 TIGR04087, YqxM_for_SipW, YqxM protein. Members of this protein,
including the partially characterized YqxM of Bacillus
subtilis, are always found adjacent to a variant form,
SipW, of signal peptidase, and are targets for this
signal peptide, as is the biofilm protein constituent
TasA. The function may always be associated with biofilm
formation. In one instance, this protein is fused with
the SipW signal peptidase.
Length = 186
Score = 29.0 bits (65), Expect = 2.4
Identities = 10/38 (26%), Positives = 17/38 (44%)
Query: 19 EKNFISSKKFNHLLLIQTEYMGGGAFQFSVYNQPSYEK 56
E+ I+ K + ++ + M G + F VY P Y
Sbjct: 126 EEGTITPLKSGSIYKLEYKAMKPGIYAFKVYQPPGYPA 163
>gnl|CDD|176773 cd08795, Death_IRAK2, Death domain of Interleukin 1 Receptor
Associated Kinase-2. Death Domain (DD) of Interleukin-1
Receptor-Associated Kinase 1 (IRAK1). IRAKs are
essential components of innate immunity and inflammation
in mammals and other vertebrates. They are involved in
signal transduction pathways involving IL-1 and IL-18
receptors, Toll-like receptors (TLRs), nuclear
factor-kappaB (NF-kB), and mitogen-activated protein
kinases (MAPKs). IRAKs contain an N-terminal DD domain
and a C-terminal kinase domain. IRAK2 is an essential
component of several signaling pathways, including
NF-kappaB and the IL-1 signaling pathways. It is an
inactive kinase that participates in septic shock
mediated by TLR4 and TLR9. It plays a redundant role
with IRAK1 in early NF-kB and MAPK responses, and
remains present at later stages whereas IRAK1
disappears. DDs are protein-protein interaction domains
found in a variety of domain architectures. Their common
feature is that they form homodimers by self-association
or heterodimers by associating with other members of the
DD superfamily including CARD (Caspase activation and
recruitment domain), DED (Death Effector Domain), and
PYRIN. They serve as adaptors in signaling pathways and
can recruit other proteins into signaling complexes.
Length = 88
Score = 27.6 bits (61), Expect = 2.4
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 12/60 (20%)
Query: 192 WDWVRFNSDVIT-----RQVKPCTR---CILTTVHPDTGRKQPDSQP----LKMLQMYRA 239
WDW+RF S VIT R++K I + G + Q L+ L++YRA
Sbjct: 24 WDWMRFASYVITDQTQLRKIKSMEWTGVSITRELMWWWGMRLATVQQLVDLLQRLELYRA 83
>gnl|CDD|182039 PRK09706, PRK09706, transcriptional repressor DicA; Reviewed.
Length = 135
Score = 27.9 bits (62), Expect = 3.3
Identities = 10/37 (27%), Positives = 19/37 (51%), Gaps = 8/37 (21%)
Query: 227 DSQPLKMLQMYRAVPDLE--------RRKVENFAPMF 255
++L+++ A+P+ E R +VENF +F
Sbjct: 86 SEDQKELLELFDALPESEQDAQLSEMRARVENFNKLF 122
>gnl|CDD|179584 PRK03501, ppnK, inorganic polyphosphate/ATP-NAD kinase;
Provisional.
Length = 264
Score = 28.4 bits (64), Expect = 4.1
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 11/64 (17%)
Query: 124 RKYTTVYDNVNDEDIGVYADMTSYMVLNENSLR-DLNKKMS-DIGVEDVSMLQFRGN-IV 180
RKY T+ V+ TS+ LNE S+R + K D+ ++D+ FRG+ +V
Sbjct: 102 RKYPTIEVTVDGS--------TSFYCLNEFSIRSSIIKTFVIDVYIDDLHFETFRGDGMV 153
Query: 181 VDGP 184
V P
Sbjct: 154 VSTP 157
>gnl|CDD|177317 PHA01752, PHA01752, hypothetical protein.
Length = 488
Score = 28.5 bits (63), Expect = 4.3
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 4/75 (5%)
Query: 58 TIQVADILQTSHTKSFTLYVDEVLEAFDCGDLASDWFAKYLLNQSDRSIRLGLSTNRRRS 117
IQ+ + T++ ++ + +L A + +LA F +Q+ + LG S N S
Sbjct: 74 NIQIPLGINTNYGIAYASIISSLLSALN--NLAISVFNPNFNSQT--FLNLGQSANFGIS 129
Query: 118 IGDNYLRKYTTVYDN 132
G N L YT++YDN
Sbjct: 130 NGINLLNNYTSLYDN 144
>gnl|CDD|133155 cd05488, Proteinase_A_fungi, Fungal Proteinase A , aspartic
proteinase superfamily. Fungal Proteinase A, a
proteolytic enzyme distributed among a variety of
organisms, is a member of the aspartic proteinase
superfamily. In Saccharomyces cerevisiae, targeted to
the vacuole as a zymogen, activation of proteinases A at
acidic pH can occur by two different pathways: a
one-step process to release mature proteinase A,
involving the intervention of proteinase B, or a
step-wise pathway via the auto-activation product known
as pseudo-proteinase A. Once active, S. cerevisiae
proteinase A is essential to the activities of other
yeast vacuolar hydrolases, including proteinase B and
carboxypeptidase Y. The mature enzyme is bilobal, with
each lobe providing one of the two catalytically
essential aspartic acid residues in the active site. The
crystal structure of free proteinase A shows that flap
loop is atypically pointing directly into the S(1)
pocket of the enzyme. Proteinase A preferentially
hydrolyzes hydrophobic residues such as Phe, Leu or Glu
at the P1 position and Phe, Ile, Leu or Ala at P1'.
Moreover, the enzyme is inhibited by IA3, a natural and
highly specific inhibitor produced by S. cerevisiae.
This family of aspartate proteases is classified by
MEROPS as the peptidase family A1 (pepsin A, clan AA).
Length = 320
Score = 28.2 bits (63), Expect = 4.9
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 118 IGDNYLRKYTTVYDNVND 135
+GD +LRKY +VYD N+
Sbjct: 297 VGDAFLRKYYSVYDLGNN 314
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 27.9 bits (63), Expect = 6.9
Identities = 8/18 (44%), Positives = 12/18 (66%), Gaps = 1/18 (5%)
Query: 128 TVYDNV-NDEDIGVYADM 144
T+YD + ED ++ADM
Sbjct: 328 TIYDEMRKTEDFKIFADM 345
>gnl|CDD|100043 cd03352, LbH_LpxD, UDP-3-O-acyl-glucosamine N-acyltransferase
(LpxD): The enzyme catalyzes the transfer of
3-hydroxymyristic acid or 3-hydroxy-arachidic acid,
depending on the organism, from the acyl carrier protein
(ACP) to UDP-3-O-acyl-glucosamine to produce
UDP-2,3-diacyl-GlcNAc. This constitutes the third step
in the lipid A biosynthetic pathway in Gram-negative
bacteria. LpxD is a homotrimer, with each subunit
consisting of a novel combination of an N-terminal
uridine-binding domain, a core lipid-binding left-handed
parallel beta helix (LbH) domain, and a C-terminal
alpha-helical extension. The LbH domain contains 9
turns, each containing three imperfect tandem repeats of
a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X).
Length = 205
Score = 27.4 bits (62), Expect = 7.1
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 250 NFAPMFGVYMGVHRTGYVNVGDDVYVGC 277
FAP G ++ + + G V +GDDV +G
Sbjct: 76 GFAPDGGGWVKIPQLGGVIIGDDVEIGA 103
>gnl|CDD|107284 cd06289, PBP1_MalI_like, Ligand-binding domain of MalI, a
transcription regulator of the maltose system of
Escherichia coli and its close homologs from other
bacteria. This group includes the ligand-binding domain
of MalI, a transcription regulator of the maltose system
of Escherichia coli and its close homologs from other
bacteria. They are members of the LacI-GalR family of
repressor proteins which are composed of two functional
domains: an N-terminal HTH (helix-turn-helix) domain,
which is responsible for the DNA-binding specificity,
and a C-terminal ligand-binding domain, which is
homologous to the sugar-binding domain of ABC-type
transport systems that contain the type I periplasmic
binding protein-like fold. As also observed in the
periplasmic binding proteins, the C-terminal domain of
the bacterial transcription repressor undergoes a
conformational change upon ligand binding which in turn
changes the DNA binding affinity of the repressor.
Length = 268
Score = 27.1 bits (61), Expect = 8.7
Identities = 11/27 (40%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 254 MFGVYMGVHRTGYVNVGDDV-YVGCDD 279
FG G+ R G + G D+ VG DD
Sbjct: 190 AFGAMSGLRRAG-LTPGRDIAVVGFDD 215
>gnl|CDD|219933 pfam08612, Med20, TATA-binding related factor (TRF) of subunit 20
of Mediator complex. This family of proteins is related
to TATA-binding protein (TBP). TBP is a highly conserved
RNA polymerase II general transcription factor that
binds to the core promoter and initiates assembly of the
preinitiation complex. Human TRF has been shown to
associate with an RNA polymerase II-SRB complex. This
Med20 subunit of Mediator is found in the non-essential
part of the head.
Length = 197
Score = 26.9 bits (60), Expect = 9.0
Identities = 23/116 (19%), Positives = 47/116 (40%), Gaps = 20/116 (17%)
Query: 9 DRSFVLFNEKEKNFISSKKFNHLLLIQTEYMGGGAFQFSVYNQPSYEKLTIQVADILQTS 68
D F L EK ++F + ++ ++ E GGG ++ ++V ++ QT+
Sbjct: 88 DSFFQLLMEKLQSFWTQRQ-----TVKGE--GGGTYE--------LGDFRVRVGNVFQTT 132
Query: 69 HTKSFTLYV----DEVLEAFDCGDLASDWFAKYLLNQSDRSIRLGLSTNRRRSIGD 120
+ + V D E C L ++ K+ +N + SI + + + D
Sbjct: 133 TFRGILVEVEYRYDPCEEFEKCRALIREFLQKFGINGAKESI-PSVGPEKLSDLYD 187
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 0.137 0.409
Gapped
Lambda K H
0.267 0.0739 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,222,617
Number of extensions: 1335411
Number of successful extensions: 1020
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1014
Number of HSP's successfully gapped: 21
Length of query: 280
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 184
Effective length of database: 6,679,618
Effective search space: 1229049712
Effective search space used: 1229049712
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: 58 (26.1 bits)