RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8153
(193 letters)
>gnl|CDD|216557 pfam01534, Frizzled, Frizzled/Smoothened family membrane region.
This family contains the membrane spanning region of
frizzled and smoothened receptors. This membrane region
is predicted to contain seven transmembrane alpha
helices. Proteins related to Drosophila frizzled are
receptors for Wnt (mediating the beta-catenin signalling
pathway), but also the planar cell polarity (PCP)
pathway and the Wnt/calcium pathway. The predominantly
alpha-helical Cys-rich ligand-binding region (CRD) of
Frizzled is both necessary and sufficient for Wnt
binding. The smoothened receptor mediates hedgehog
signalling.
Length = 328
Score = 152 bits (385), Expect = 2e-45
Identities = 59/109 (54%), Positives = 79/109 (72%)
Query: 52 NPLEGDILTGVCYVGIWNRQALWDFVIIPLSIYLILGLVFLFTGFISLLRIRTIMKHDGT 111
N ++GD L+G+C+VG N AL FV+ PL +YL++G FL GF+SL RIR+++K DGT
Sbjct: 158 NKVDGDELSGICFVGNLNLDALRGFVLAPLCLYLVIGTSFLLAGFVSLFRIRSVIKTDGT 217
Query: 112 KTDKLEKLMIRICIFSVLYTVPAVLVIVCYLYEFVYIDYWMLTWHVDMC 160
T KLEKLM+RI +FS+LYTVPA++VI CY YEF D W +W +C
Sbjct: 218 NTSKLEKLMVRIGVFSILYTVPALIVIACYFYEFANRDEWERSWRDCIC 266
>gnl|CDD|239587 cd03510, Rhizobitoxine-FADS-like, This CD includes the
dihydrorhizobitoxine fatty acid desaturase (RtxC)
characterized in Bradyrhizobium japonicum USDA110, and
other related proteins. Dihydrorhizobitoxine desaturase
is reported to be involved in the final step of
rhizobitoxine biosynthesis. This domain family appears
to be structurally related to the membrane fatty acid
desaturases and the alkane hydroxylases. They all share
in common extensive hydrophobic regions that would be
capable of spanning the membrane bilayer at least twice.
Comparison of sequences also reveals the existence of
three regions of conserved histidine cluster motifs that
contain eight histidine residues: HXXXH, HXX(X)HH, and
HXXHH. These histidine residues are reported to be
catalytically essential and proposed to be the ligands
for the iron atoms contained within homologs, stearoyl
CoA desaturase and alkane hydroxylase.
Length = 175
Score = 31.1 bits (71), Expect = 0.20
Identities = 16/34 (47%), Positives = 21/34 (61%)
Query: 81 LSIYLILGLVFLFTGFISLLRIRTIMKHDGTKTD 114
L++YL+L LV L T F + RIR I +H G D
Sbjct: 92 LALYLLLWLVPLLTVFPLIGRIREIAEHAGVPAD 125
>gnl|CDD|236394 PRK09169, PRK09169, hypothetical protein; Validated.
Length = 2316
Score = 32.0 bits (73), Expect = 0.21
Identities = 16/38 (42%), Positives = 19/38 (50%), Gaps = 5/38 (13%)
Query: 13 GRERLLRTGVRSRHWLELLEDPSEQRSKLEELEELQHL 50
G ER LR G+R LLE +E L+EL E L
Sbjct: 1636 GTERELRRGLR-----RLLEGEAEAPQALQELRERARL 1668
>gnl|CDD|216883 pfam02118, Srg, Srg family chemoreceptor.
Length = 275
Score = 29.5 bits (67), Expect = 0.96
Identities = 18/81 (22%), Positives = 32/81 (39%), Gaps = 10/81 (12%)
Query: 67 IWNRQALWDFVIIPLSIYLILGLVFLFTGFISLLRIRTIMKHDGTKTDKLEKLMIRICIF 126
W +L+ IY IL LVF I+ + + + +E+ + I IF
Sbjct: 165 PWASTSLF------QLIYFILILVF---TIITSIVTSYKLAKLSKRIKSVERSLTIITIF 215
Query: 127 -SVLYTVPAVLVIVCYLYEFV 146
SV++ + A ++ F
Sbjct: 216 ISVVFLLVAAWQVLNSFAFFF 236
>gnl|CDD|220666 pfam10269, Tmemb_185A, Transmembrane Fragile-X-F protein. This is
a family of conserved transmembrane proteins that appear
in humans to be expressed from a region upstream of the
FragileXF site and to be intimately linked with the
Fragile-X syndrome. Absence of TMEM185A does not
necessarily lead to developmental delay, but might in
combination with other, yet unknown, factors. Otherwise,
the lack of the TMEM185A protein is either disposable
(redundant) or its function can be complemented by the
highly similar chromosome 2 retro-pseudogene product,
TMEM185B.
Length = 226
Score = 28.5 bits (64), Expect = 1.7
Identities = 15/66 (22%), Positives = 30/66 (45%), Gaps = 2/66 (3%)
Query: 74 WDFVIIPLSIYLILGLVFLFTGFISLLRIRTIMKHDGTKTDKLEKLMIRICIFSVLYTVP 133
W V IPL I L L + + ++ ++ IR + +++ + L I S+ +P
Sbjct: 139 WWVVFIPLWIVLGLAFLVVL--YLVIMSIRLLRENNLLVSQDERALASAIGYLSIFIVIP 196
Query: 134 AVLVIV 139
++ V
Sbjct: 197 MLVFQV 202
>gnl|CDD|222043 pfam13314, DUF4083, Domain of unknown function (DUF4083). This is
a family of very short, approximately 60 residue,
proteins from Firmicutes, that are all putatively
annotated as being MutT/Nudix. However, the
characteristic Nudix motif of GX(5)EX(7)REUXEE is
absent.
Length = 58
Score = 26.6 bits (59), Expect = 2.1
Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 73 LWDFVIIPLSIYLILGLVFLFTGFISLLRIRTIMK--HDGTKTDKLEKLM 120
L + + + I LI+ + FT FI L + K H KL++++
Sbjct: 3 LGTSIYLIVVIILIVLIGASFTLFIRRLLHTSAAKKQHSDPIEQKLDRII 52
>gnl|CDD|176207 cd08245, CAD, Cinnamyl alcohol dehydrogenases (CAD) and related
proteins. Cinnamyl alcohol dehydrogenases (CAD),
members of the medium chain dehydrogenase/reductase
family, reduce cinnamaldehydes to cinnamyl alcohols in
the last step of monolignal metabolism in plant cells
walls. CAD binds 2 zinc ions and is NADPH- dependent.
CAD family members are also found in non-plant species,
e.g. in yeast where they have an aldehyde reductase
activity. The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class
I mammalian ADH. MDRs display a broad range of
activities and are distinguished from the smaller short
chain dehydrogenases (~ 250 amino acids vs. the ~ 350
amino acids of the MDR). The MDR proteins have 2
domains: a C-terminal NAD(P) binding-Rossmann fold
domain of a beta-alpha form and an N-terminal catalytic
domain with distant homology to GroES. The MDR group
contains a host of activities, including the founding
alcohol dehydrogenase (ADH), quinone reductase,
sorbitol dehydrogenase, formaldehyde dehydrogenase,
butanediol DH, ketose reductase, cinnamyl reductase,
and numerous others. The zinc-dependent alcohol
dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent
interconversion of alcohols to aldehydes, or ketones.
Active site zinc has a catalytic role, while structural
zinc aids in stability. ADH-like proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and generally have 2
tightly bound zinc atoms per subunit. The active site
zinc is coordinated by a histidine, two cysteines, and
a water molecule. The second zinc seems to play a
structural role, affects subunit interactions, and is
typically coordinated by 4 cysteines.
Length = 330
Score = 28.1 bits (63), Expect = 3.1
Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 6/44 (13%)
Query: 43 ELEELQHLPNPLEGDIL-----TGVCYVGIWNRQALWDFVIIPL 81
E EE+ +P P G++L GVC+ + + W PL
Sbjct: 13 EPEEVP-VPEPGPGEVLIKIEACGVCHTDLHAAEGDWGGSKYPL 55
>gnl|CDD|214492 smart00055, FCH, Fes/CIP4 homology domain. Alignment extended
from original report. Highly alpha-helical. Also known
as the RAEYL motif or the S. pombe Cdc15 N-terminal
domain.
Length = 87
Score = 26.5 bits (59), Expect = 3.7
Identities = 18/62 (29%), Positives = 25/62 (40%), Gaps = 2/62 (3%)
Query: 8 FTGDSGRERLLRTGVRSRHWLELLEDPSEQRSKLEE--LEELQHLPNPLEGDILTGVCYV 65
D G E LL LE L+ +R+K+EE ++LQ L L T Y
Sbjct: 5 SELDDGFEALLSRLKNGLRLLEDLKKFMRERAKIEEEYAKKLQKLSKKLRAVRDTEPEYG 64
Query: 66 GI 67
+
Sbjct: 65 SL 66
>gnl|CDD|239003 cd02048, neuroserpin, Neuroserpin is a inhibitory member of the
SERine Proteinase INhibitor (serpin) family that reacts
preferentially with tissue-type plasminogen activator
(tPA). It is located in neurons in regions of the brain
where tPA is also found, suggesting that neuroserpin is
the selective inhibitor of tPA in the central nervous
system (CNS). This subgroup corresponds to clade I of
the serpin superfamily.
Length = 388
Score = 27.1 bits (60), Expect = 5.7
Identities = 14/33 (42%), Positives = 18/33 (54%)
Query: 80 PLSIYLILGLVFLFTGFISLLRIRTIMKHDGTK 112
PLS L LG+V L +L IR + +DG K
Sbjct: 28 PLSTALALGMVELGAKGSALKEIRHSLGYDGLK 60
>gnl|CDD|219562 pfam07766, LETM1, LETM1-like protein. Members of this family are
inner mitochondrial membrane proteins which play a role
in potassium and hydrogen ion exchange. Deletion of
LETM1 is thought to be involved in the development of
Wolf-Hirschhorn syndrome in humans.
Length = 268
Score = 26.9 bits (60), Expect = 6.0
Identities = 11/50 (22%), Positives = 20/50 (40%), Gaps = 8/50 (16%)
Query: 76 FVIIPLSIYLILGLVFLFTGFISLLRIRTIMKHDGTKTDKLEKLMIRICI 125
F+I+P + L+ + LF + T T + EKL + +
Sbjct: 66 FIIVPFAELLLPIALKLFPNMLP--------STFWTATQREEKLKKLLKV 107
>gnl|CDD|226259 COG3736, VirB8, Type IV secretory pathway, component VirB8
[Intracellular trafficking and secretion].
Length = 239
Score = 26.6 bits (59), Expect = 7.8
Identities = 17/73 (23%), Positives = 24/73 (32%), Gaps = 13/73 (17%)
Query: 112 KTDKLEK---LMIRICIFSVLYTVPAVLVIVCYL----YEFVYIDYWMLTWHVDMCSGTS 164
+ KLE+ L R+ I L V AV+ I L E + T +V
Sbjct: 32 RVIKLERSRRLAWRVAILFTLLAVAAVIAIAILLPLKKTEPYVVRVDNNTGNVA------ 85
Query: 165 SVSSLSKPMTSSY 177
V L +
Sbjct: 86 IVQRLDSSPITYD 98
>gnl|CDD|238832 cd01662, Ubiquinol_Oxidase_I, Ubiquinol oxidase subunit I.
Ubiquinol oxidase, the terminal oxidase in the
respiratory chains of aerobic bacteria, is a multi-chain
transmembrane protein located in the cell membrane. It
catalyzes the reduction of O2 and simultaneously pumps
protons across the membrane. The number of subunits in
ubiquinol oxidase varies from two to five. Subunit I
contains a heme-copper binuclear center (the active site
where O2 is reduced to water) formed by a high-spin heme
and a copper ion. It also contains a low-spin heme,
believed to participate in the transfer of electrons
from ubiquinol to the binuclear center. For every
reduction of an O2 molecule, eight protons are taken
from the inside aqueous compartment and four electrons
are taken from ubiquinol on the opposite side of the
membrane. The four electrons and four of the protons
are used in the reduction of O2; the four remaining
protons are pumped across the membrane. This charge
separation of four charges contributes to the
electrochemical gradient used for ATP synthesis. Two
proton channels, the D-pathway and K-pathway, leading to
the binuclear center have been identified in subunit I.
It is generally believed that the channels contain water
molecules that act as 'proton wires' to transfer the
protons. A well-defined pathway for the transfer of
pumped protons beyond the binuclear center has not been
identified. Electrons are believed to be transferred
directly from ubiquinol (the electron donor) to the
low-spin heme, and directly from the low-spin heme to
the binuclear center.
Length = 501
Score = 26.8 bits (60), Expect = 8.0
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 84 YLILGLVFLFTGFISLLRIRT 104
Y+I VF G + L +RT
Sbjct: 14 YIITAFVFFLRGGVDALLMRT 34
>gnl|CDD|234038 TIGR02865, spore_II_E, stage II sporulation protein E. Stage II
sporulation protein E (SpoIIE) is a multiple membrane
spanning protein with two separable functions. It plays
a role in the switch to polar cell division during
sporulation. By means of it protein phosphatase
activity, located in the C-terminal region, it activates
sigma-F. All proteins that score above the trusted
cutoff to this model are found in endospore-forming
Gram-positive bacteria. Surprisingly, a sequence from
the Cyanobacterium-like (and presumably
non-spore-forming) photosynthesizer Heliobacillus
mobilis is homologous, and scores between the trusted
and noise cutoffs [Cellular processes, Sporulation and
germination].
Length = 764
Score = 27.0 bits (60), Expect = 8.3
Identities = 25/110 (22%), Positives = 38/110 (34%), Gaps = 27/110 (24%)
Query: 78 IIPLSIYLILGLVFLFTGFISLLRIRTIMKHDGTKTDKLEKLMIRICIFSVLYTVPAVLV 137
I P L LV + +L+ TDK + V++ AV
Sbjct: 54 IQPKHSLKYLLLVAVIILLSYVLK---------NLTDK----KKTVVPPIVVFLEAAVYA 100
Query: 138 IVCYLYEFVY--IDYWMLTWHVDMCSGTSSVSSLSKPMTSSYNNIYSIPC 185
I YL + +D+ + +SLS + +N YSIPC
Sbjct: 101 IFGYLQNKLVTPLDFILSIVE----------ASLSFVLYYIFN--YSIPC 138
>gnl|CDD|235604 PRK05778, PRK05778, 2-oxoglutarate ferredoxin oxidoreductase
subunit beta; Validated.
Length = 301
Score = 26.8 bits (60), Expect = 8.8
Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 5/38 (13%)
Query: 28 LELLEDPSEQRSKLEELEELQHLPNPLEGDILTGVCYV 65
LE DP+++ E++ E + L G I GV Y
Sbjct: 233 LEEDYDPTDRDKAAEKMLEEE-----LGGKIPIGVFYK 265
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 26.8 bits (60), Expect = 8.9
Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 2/77 (2%)
Query: 77 VIIPLSIYLILGLVFLFTGFISLLRIRTIMKHDGTKTDKLEKLMIRICIFSVLYTVPAVL 136
V+ L I L++G++ LF G + L ++ K L +L + + +L V
Sbjct: 442 VMTILIISLLIGVIHLFLGLL--LGFINNVRKGDYKDAFLAQLGWLLILLGILLIVLGGF 499
Query: 137 VIVCYLYEFVYIDYWML 153
+V L I +++
Sbjct: 500 GLVVGLGPLGLIGKYLI 516
>gnl|CDD|235682 PRK06041, PRK06041, flagellar assembly protein J; Reviewed.
Length = 553
Score = 26.8 bits (60), Expect = 9.4
Identities = 15/82 (18%), Positives = 28/82 (34%), Gaps = 8/82 (9%)
Query: 77 VIIPLSIYLILGLVFLFTGFISLLRIRTIMK--------HDGTKTDKLEKLMIRICIFSV 128
++ L L FI + + I K H K +K + ++ I SV
Sbjct: 212 ILTGTDPTTTLSLSLFLFLFIEVGGVYVIKKRVPKDPLWHTLEIKTKEQKKIRKLLIISV 271
Query: 129 LYTVPAVLVIVCYLYEFVYIDY 150
+ VL+++ + I
Sbjct: 272 PLSAILVLLLLLLGFIIGPILI 293
>gnl|CDD|223250 COG0172, SerS, Seryl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 26.4 bits (59), Expect = 9.7
Identities = 19/45 (42%), Positives = 25/45 (55%)
Query: 14 RERLLRTGVRSRHWLELLEDPSEQRSKLEELEELQHLPNPLEGDI 58
RE+L + G + +LLE E+R L ELEELQ N L +I
Sbjct: 15 REKLKKRGGDALDVDKLLELDEERRKLLRELEELQAERNELSKEI 59
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
0.327 0.142 0.448
Gapped
Lambda K H
0.267 0.0714 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,145,748
Number of extensions: 972183
Number of successful extensions: 1887
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1871
Number of HSP's successfully gapped: 84
Length of query: 193
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 101
Effective length of database: 6,857,034
Effective search space: 692560434
Effective search space used: 692560434
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 56 (25.4 bits)