RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11251
(190 letters)
>gnl|CDD|153305 cd07621, BAR_SNX5_6, The Bin/Amphiphysin/Rvs (BAR) domain of
Sorting Nexins 5 and 6. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions. Sorting
nexins (SNXs) are Phox homology (PX) domain containing
proteins that are involved in regulating membrane
traffic and protein sorting in the endosomal system.
SNXs differ from each other in their lipid-binding
specificity, subcellular localization and specific
function in the endocytic pathway. A subset of SNXs also
contain BAR domains. The PX-BAR structural unit
determines the specific membrane targeting of SNXs.
Members of this subfamily include SNX5, SNX6, the
mammalian SNX32, and similar proteins. SNX5 and SNX6 may
be components of the retromer complex, a membrane coat
multimeric complex required for endosomal retrieval of
lysosomal hydrolase receptors to the Golgi, acting as a
mammalian equivalent of yeast Vsp17p. The function of
SNX32 is still unknown. BAR domains form dimers that
bind to membranes, induce membrane bending and
curvature, and may also be involved in protein-protein
interactions.
Length = 219
Score = 150 bits (380), Expect = 8e-46
Identities = 58/69 (84%), Positives = 64/69 (92%)
Query: 121 AETLEKLRKVEGRIACDEDLKLSDTLRYYMRDSDAAKRLLYRRLRCLADYENANRNLERA 180
AET EKLRK+EGR+A DEDLKLSDTLRYYMRD+ AAK LLYRRLRCLA+YENAN+NLE+A
Sbjct: 87 AETFEKLRKLEGRVASDEDLKLSDTLRYYMRDTQAAKDLLYRRLRCLANYENANKNLEKA 146
Query: 181 RTKNKDVHA 189
R KNKDVHA
Sbjct: 147 RAKNKDVHA 155
>gnl|CDD|153347 cd07663, BAR_SNX5, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexin 5. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions. Sorting nexins (SNXs)
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. SNX5, abundantly expressed in
macrophages, regulates macropinocytosis, a process that
enables cells to internalize large amounts of external
solutes. It may also be a component of the retromer
complex, a membrane coat multimeric complex required for
endosomal retrieval of lysosomal hydrolase receptors to
the Golgi, acting as a mammalian equivalent of yeast
Vsp17p. It also binds the Fanconi anaemia
complementation group A protein (FANCA). SNX5 is
localized to a subdomain of early endosome and is
recruited to the plasma membrane following EGF
stimulation and elevation of PI(3,4)P2 levels. BAR
domains form dimers that bind to membranes, induce
membrane bending and curvature, and may also be involved
in protein-protein interactions.
Length = 218
Score = 102 bits (256), Expect = 2e-27
Identities = 44/67 (65%), Positives = 55/67 (82%)
Query: 121 AETLEKLRKVEGRIACDEDLKLSDTLRYYMRDSDAAKRLLYRRLRCLADYENANRNLERA 180
AE EKLRKVE R+A D+DLKL++ LRYYM + +AAK LLYRR R LADYEN+N+ L++A
Sbjct: 86 AELFEKLRKVEDRVASDQDLKLTELLRYYMLNIEAAKDLLYRRARALADYENSNKALDKA 145
Query: 181 RTKNKDV 187
R K+KDV
Sbjct: 146 RLKSKDV 152
>gnl|CDD|153346 cd07662, BAR_SNX6, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexin 6. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions. Sorting nexins (SNXs)
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. SNX6 forms a stable complex with SNX1
and may be a component of the retromer complex, a
membrane coat multimeric complex required for endosomal
retrieval of lysosomal hydrolase receptors to the Golgi,
acting as a mammalian equivalent of yeast Vsp17p. It
interacts with the receptor serine/threonine kinases
from the transforming growth factor-beta family. It also
plays roles in enhancing the degradation of EGFR and in
regulating the activity of Na,K-ATPase through its
interaction with Translationally Controlled Tumor
Protein (TCTP). BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 218
Score = 95.9 bits (238), Expect = 8e-25
Identities = 44/67 (65%), Positives = 54/67 (80%)
Query: 121 AETLEKLRKVEGRIACDEDLKLSDTLRYYMRDSDAAKRLLYRRLRCLADYENANRNLERA 180
+E +K RK+E R+A DEDLKLSD L+YY+R+S AAK LLYRR R L DYENAN+ L++A
Sbjct: 86 SELFDKTRKIEARVAADEDLKLSDLLKYYLRESQAAKDLLYRRSRSLVDYENANKALDKA 145
Query: 181 RTKNKDV 187
R KNKDV
Sbjct: 146 RAKNKDV 152
>gnl|CDD|201356 pfam00628, PHD, PHD-finger. PHD folds into an interleaved type
of Zn-finger chelating 2 Zn ions in a similar manner to
that of the RING and FYVE domains. Several PHD fingers
have been identified as binding modules of methylated
histone H3.
Length = 51
Score = 51.3 bits (123), Expect = 1e-09
Identities = 24/47 (51%), Positives = 31/47 (65%), Gaps = 2/47 (4%)
Query: 54 CSVCGTSDNDDQLLFCDDCDRGYHMYCLVPPIQT--PPEGSWSCQLC 98
C+VCG D+D +LL CD CDR +H+ CL PP++ PEG W C C
Sbjct: 2 CAVCGKVDDDGELLLCDGCDRWFHLACLGPPLEPEEIPEGEWYCPEC 48
Score = 34.4 bits (79), Expect = 0.002
Identities = 13/46 (28%), Positives = 18/46 (39%), Gaps = 1/46 (2%)
Query: 9 KSGQPEDLVSCSDCGRSGHPTCLQFTNNMKVSVKQYRWQCIECKCC 54
K +L+ C C R H CL + + + W C ECK
Sbjct: 7 KVDDDGELLLCDGCDRWFHLACLGPPLEPEE-IPEGEWYCPECKPK 51
>gnl|CDD|214584 smart00249, PHD, PHD zinc finger. The plant homeodomain (PHD)
finger is a C4HC3 zinc-finger-like motif found in
nuclear proteins thought to be involved in epigenetics
and chromatin-mediated transcriptional regulation. The
PHD finger binds two zinc ions using the so-called
'cross-brace' motif and is thus structurally related to
the RING finger and the FYVE finger. It is not yet
known if PHD fingers have a common molecular function.
Several reports suggest that it can function as a
protein-protein interacton domain and it was recently
demonstrated that the PHD finger of p300 can cooperate
with the adjacent BROMO domain in nucleosome binding in
vitro. Other reports suggesting that the PHD finger is
a ubiquitin ligase have been refuted as these domains
were RING fingers misidentified as PHD fingers.
Length = 47
Score = 47.6 bits (113), Expect = 4e-08
Identities = 24/46 (52%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 54 CSVCGTSDNDDQLLFCDDCDRGYHMYCLVPPIQT-PPEGSWSCQLC 98
CSVCG D+ +LL CD CDR YH CL PP+ P+G W C C
Sbjct: 2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
Score = 32.2 bits (73), Expect = 0.013
Identities = 12/43 (27%), Positives = 17/43 (39%), Gaps = 2/43 (4%)
Query: 9 KSGQPEDLVSCSDCGRSGHPTCLQFTNNMKVSVKQYRWQCIEC 51
K +L+ C C R H TCL + +W C +C
Sbjct: 7 KPDDGGELLQCDGCDRWYHQTCLGPP--LLEEEPDGKWYCPKC 47
>gnl|CDD|153280 cd07596, BAR_SNX, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexins. BAR domains are dimerization, lipid binding and
curvature sensing modules found in many different
proteins with diverse functions. Sorting nexins (SNXs)
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 218
Score = 44.3 bits (105), Expect = 7e-06
Identities = 15/63 (23%), Positives = 28/63 (44%)
Query: 121 AETLEKLRKVEGRIACDEDLKLSDTLRYYMRDSDAAKRLLYRRLRCLADYENANRNLERA 180
+ E+L + A E +KL + L+ Y+R A K L R L ++ ++L
Sbjct: 70 GKAAEELSSLSEAQANQELVKLLEPLKEYLRYCQAVKETLDDRADALLTLQSLKKDLASK 129
Query: 181 RTK 183
+ +
Sbjct: 130 KAQ 132
>gnl|CDD|240069 cd04718, BAH_plant_2, BAH, or Bromo Adjacent Homology domain,
plant-specific sub-family with unknown function. BAH
domains are found in a variety of proteins playing roles
in transcriptional silencing and the remodeling of
chromatin. It is assumed that in most or all of these
instances the BAH domain mediates protein-protein
interactions.
Length = 148
Score = 41.4 bits (97), Expect = 4e-05
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 75 GYHMYCLVPPIQTPPEGSWSCQLCLKE 101
G+H+ CL PP++ PEG W C C E
Sbjct: 1 GFHLCCLRPPLKEVPEGDWICPFCEVE 27
>gnl|CDD|227470 COG5141, COG5141, PHD zinc finger-containing protein [General
function prediction only].
Length = 669
Score = 40.7 bits (95), Expect = 2e-04
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 41 VKQYRWQCIECKCCSVCGTSDNDDQ--LLFCDDCDRGYHMYCLVPPIQTPPEGSWSCQLC 98
V+ C+ C ++ N++ ++FCD C+ H C IQ PEG W C+ C
Sbjct: 183 VEPIEPSDEFDDICTKCTSTHNENSNAIVFCDGCEICVHQSCY--GIQFLPEGFWLCRKC 240
Query: 99 L 99
+
Sbjct: 241 I 241
>gnl|CDD|220180 pfam09325, Vps5, Vps5 C terminal like. Vps5 is a sorting nexin
that functions in membrane trafficking. This is the C
terminal dimerisation domain.
Length = 236
Score = 39.2 bits (92), Expect = 5e-04
Identities = 16/63 (25%), Positives = 36/63 (57%)
Query: 121 AETLEKLRKVEGRIACDEDLKLSDTLRYYMRDSDAAKRLLYRRLRCLADYENANRNLERA 180
AE E+++++ R A + L L +T+ Y+R + K + +R++ ++NA ++L +
Sbjct: 88 AEVEERIKELLERQALQDVLTLGETIDEYLRLIGSVKAVFNQRVKAWQQWQNAEQDLSKK 147
Query: 181 RTK 183
R +
Sbjct: 148 RAQ 150
>gnl|CDD|153314 cd07630, BAR_SNX_like, The Bin/Amphiphysin/Rvs (BAR) domain of
uncharacterized Sorting Nexins. BAR domains are
dimerization, lipid binding and curvature sensing
modules found in many different proteins with diverse
functions. This subfamily is composed of uncharacterized
proteins with similarity to sorting nexins (SNXs), which
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 198
Score = 36.7 bits (85), Expect = 0.003
Identities = 19/54 (35%), Positives = 34/54 (62%)
Query: 134 IACDEDLKLSDTLRYYMRDSDAAKRLLYRRLRCLADYENANRNLERARTKNKDV 187
+A + + L TL Y R S++ K +L+RR L ++ENA++ LE+A+ + K+
Sbjct: 83 VAGNNENTLGLTLDLYSRYSESEKDMLFRRTCKLIEFENASKALEKAKPQKKEQ 136
>gnl|CDD|153307 cd07623, BAR_SNX1_2, The Bin/Amphiphysin/Rvs (BAR) domain of
Sorting Nexins 1 and 2. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions. Sorting
nexins (SNXs) are Phox homology (PX) domain containing
proteins that are involved in regulating membrane
traffic and protein sorting in the endosomal system.
SNXs differ from each other in their lipid-binding
specificity, subcellular localization and specific
function in the endocytic pathway. A subset of SNXs also
contain BAR domains. The PX-BAR structural unit
determines the specific membrane targeting of SNXs. This
subfamily consists of SNX1, SNX2, and similar proteins.
SNX1 and SNX2 are components of the retromer complex, a
membrane coat multimeric complex required for endosomal
retrieval of lysosomal hydrolase receptors to the Golgi.
The retromer consists of a cargo-recognition subcomplex
and a subcomplex formed by a dimer of sorting nexins
(SNX1 and/or SNX2), which ensures efficient cargo
sorting by facilitating proper membrane localization of
the cargo-recognition subcomplex. BAR domains form
dimers that bind to membranes, induce membrane bending
and curvature, and may also be involved in
protein-protein interactions.
Length = 224
Score = 31.1 bits (71), Expect = 0.28
Identities = 18/62 (29%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 121 AETLEKLRKVEGRIACDEDL-KLSDTLRYYMRDSDAAKRLLYRRLRCLADYENANRNLER 179
AE EK+ ++ G A D D L++ L+ Y+ A K + + R++ +++NA + L +
Sbjct: 76 AEVEEKIEQLHGEQA-DTDFYILAELLKDYIGLIGAIKDVFHERVKVWQNWQNAQQTLTK 134
Query: 180 AR 181
R
Sbjct: 135 KR 136
>gnl|CDD|185749 cd09236, V_AnPalA_UmRIM20_like, Protein-interacting V-domains of
Aspergillus nidulans PalA/RIM20, Ustilago maydis RIM20,
and related proteins. This family belongs to the
V_Alix_like superfamily which includes the V-shaped (V)
domains of Bro1 and Rim20 from Saccharomyces cerevisiae,
mammalian Alix (apoptosis-linked gene-2 interacting
protein X), His-Domain type N23 protein tyrosine
phosphatase (HD-PTP, also known as PTPN23), and related
domains. Aspergillus nidulas PalA/RIM20 and Ustilago
maydis RIM20, like Saccharomyces cerevisiae Rim20,
participate in the response to the external pH via the
Pal/Rim101 pathway; however, Saccharomyces cerevisiae
Rim20 does not belong to this family. This pathway is a
signaling cascade resulting in the activation of the
transcription factor PacC/Rim101. The mammalian Alix
V-domain (belonging to a different family) contains a
binding site, partially conserved in the superfamily,
for the retroviral late assembly (L) domain YPXnL motif.
Aspergillus nidulas PalA binds a nonviral YPXnL motif
(tandem YPXL/I motifs within PacC). The Alix V-domain is
also a dimerization domain. In addition to this
V-domain, members of the V_Alix_like superfamily also
have an N-terminal Bro1-like domain, which has been
shown to bind CHMP4/Snf7, a component of the ESCRT-III
complex.
Length = 353
Score = 29.6 bits (67), Expect = 0.87
Identities = 13/45 (28%), Positives = 18/45 (40%), Gaps = 1/45 (2%)
Query: 138 EDLKLSDTLRYYMRDSDAAKRLLYRRLRCLADYENANRNLERART 182
EDL L Y +D DA + L E AN+ ++R
Sbjct: 253 EDL-FDKRLAKYDKDLDAVSEEAQEQEEILQQIEVANKAFLQSRK 296
>gnl|CDD|131764 TIGR02717, AcCoA-syn-alpha, acetyl coenzyme A synthetase (ADP
forming), alpha domain. Although technically
reversible, it is believed that this group of
ADP-dependent acetyl-CoA synthetases (ACS) act in the
direction of acetate and ATP production in the organisms
in which it has been characterized. In most species this
protein exists as a fused alpha-beta domain polypeptide.
In Pyrococcus and related species, however the domains
exist as separate polypeptides. This model represents
the alpha (N-terminal) domain. In Pyrococcus and related
species there appears to have been the development of a
paralogous family such that four other proteins are
close relatives. In reference , one of these (along with
its beta-domain partner) was characterized as ACS-II
showing specificity for phenylacetyl-CoA. This model has
been constructed to exclude these non-ACS-I paralogs.
This may result in new, authentic ACS-I sequences
falling below the trusted cutoff.
Length = 447
Score = 29.6 bits (67), Expect = 0.94
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 7/54 (12%)
Query: 139 DLKLSDTLRYYMRDSDAAKRLLYRRLRCLADYENANRNLERAR--TKNKDVHAL 190
D+ SD L Y D D LLY L ++ + L+ AR +K K + L
Sbjct: 188 DIDESDLLEYLADDPDTKVILLY-----LEGIKDGRKFLKTAREISKKKPIVVL 236
>gnl|CDD|227367 COG5034, TNG2, Chromatin remodeling protein, contains PhD zinc
finger [Chromatin structure and dynamics].
Length = 271
Score = 29.5 bits (66), Expect = 1.1
Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 5/40 (12%)
Query: 65 QLLFCD--DCDRG-YHMYCLVPPIQTPPEGSWSCQLCLKE 101
Q++ CD +C R +H+ C+ ++ PP+G W C C K
Sbjct: 233 QMVACDNANCKREWFHLECV--GLKEPPKGKWYCPECKKA 270
>gnl|CDD|227285 COG4949, COG4949, Uncharacterized membrane-anchored protein
conserved in bacteria [Function unknown].
Length = 424
Score = 29.5 bits (66), Expect = 1.1
Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 10/76 (13%)
Query: 106 IEQGRTVLKIGGFLPAETLE-KLRKVEGRIACDEDLKLSDTLRYYMRDSDAAKRLLYRRL 164
IE RT L + G A+TL ++R++E R+A S T R + ++ LL
Sbjct: 196 IETYRT-LAMLGLPLAQTLSPEIRRIEDRLA-------SITQRMKTGERRDSQALLAELT 247
Query: 165 RCLADYE-NANRNLER 179
R A+ E A +L R
Sbjct: 248 RLAAELEARAALSLYR 263
>gnl|CDD|225883 COG3346, COG3346, Uncharacterized conserved protein [Function
unknown].
Length = 252
Score = 28.9 bits (65), Expect = 1.7
Identities = 19/84 (22%), Positives = 26/84 (30%), Gaps = 17/84 (20%)
Query: 107 EQGRTVLKIGGFLPAET----------LEKLRKVEGRIACDEDLKLSDTLRYYMRDSDAA 156
+ GRTVL GF+P E + G L+ + + D+D
Sbjct: 111 DDGRTVLVNRGFVPRERKEASPRAEGQPAGPVTITGL------LRPPEPGGSLLPDNDPG 164
Query: 157 KRLLY-RRLRCLADYENANRNLER 179
K L Y L A L
Sbjct: 165 KNLWYSIDLAAFAQATGLPDLLAP 188
>gnl|CDD|223924 COG0855, Ppk, Polyphosphate kinase [Inorganic ion transport and
metabolism].
Length = 696
Score = 28.8 bits (65), Expect = 1.8
Identities = 10/49 (20%), Positives = 22/49 (44%)
Query: 104 RKIEQGRTVLKIGGFLPAETLEKLRKVEGRIACDEDLKLSDTLRYYMRD 152
R+IE G G P E L ++++ ++ ++D ++ L +
Sbjct: 63 RQIEAGIEQRSPDGLTPREQLGRIQERVLKLVQEQDRLFNELLLPLLAK 111
>gnl|CDD|222406 pfam13831, PHD_2, PHD-finger. PHD folds into an interleaved type
of Zn-finger chelating 2 Zn ions in a similar manner to
that of the RING and FYVE domains. Several PHD fingers
have been identified as binding modules of methylated
histone H3.
Length = 33
Score = 25.7 bits (57), Expect = 2.4
Identities = 10/35 (28%), Positives = 14/35 (40%), Gaps = 2/35 (5%)
Query: 64 DQLLFCDDCDRGYHMYCLVPPIQTPPEGSWSCQLC 98
+ LL C C H C + +G W C+ C
Sbjct: 1 NPLLVCSKCSVAVHASCY--GVPELSDGPWLCRRC 33
>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC;
Provisional.
Length = 695
Score = 28.4 bits (64), Expect = 2.5
Identities = 7/11 (63%), Positives = 8/11 (72%), Gaps = 1/11 (9%)
Query: 48 CIECKCCS-VC 57
CIEC C+ VC
Sbjct: 411 CIECGACAYVC 421
>gnl|CDD|166628 PLN02987, PLN02987, Cytochrome P450, family 90, subfamily A.
Length = 472
Score = 28.4 bits (63), Expect = 2.5
Identities = 16/38 (42%), Positives = 21/38 (55%)
Query: 92 SWSCQLCLKEFHRKIEQGRTVLKIGGFLPAETLEKLRK 129
SWS ++ L E +KI TV ++ F P E E LRK
Sbjct: 159 SWSSRVLLMEEAKKITFELTVKQLMSFDPGEWTESLRK 196
>gnl|CDD|148326 pfam06656, Tenui_PVC2, Tenuivirus PVC2 protein. This family
consists of several Tenuivirus PVC2 proteins from Rice
grassy stunt virus, Maize stripe virus and Rice hoja
blanca virus. The function of this family is unknown.
Length = 785
Score = 28.6 bits (64), Expect = 2.6
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 4/56 (7%)
Query: 31 LQFTNNMKVSVKQYRWQCIECKCCSVCGTS---DNDDQLLFCDDCDRGYHMYCLVP 83
L +TN+ K + + W+C E + CS G+ D D L + D C +H++ P
Sbjct: 402 LYYTNSYKRVITREDWKCFEGEGCSTDGSKSIWDKSDSLHY-DYCVEDFHVFSYCP 456
>gnl|CDD|235273 PRK04301, radA, DNA repair and recombination protein RadA;
Validated.
Length = 317
Score = 27.9 bits (63), Expect = 2.9
Identities = 12/29 (41%), Positives = 15/29 (51%)
Query: 106 IEQGRTVLKIGGFLPAETLEKLRKVEGRI 134
IE R IGGF A + + RK G+I
Sbjct: 56 IEAAREAADIGGFETALEVLERRKNVGKI 84
>gnl|CDD|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein,
contains RING Zn-finger [Posttranslational modification,
protein turnover, chaperones / Intracellular trafficking
and secretion].
Length = 190
Score = 27.5 bits (61), Expect = 3.2
Identities = 19/82 (23%), Positives = 30/82 (36%), Gaps = 16/82 (19%)
Query: 9 KSGQPEDLVSCSDCGRSGH-----PTCLQFTNNMKVSVKQYRWQCIECKCCSVCGT---- 59
S E+ C +CG++GH P + + + C + K C CG
Sbjct: 53 VSAIREENPVCFNCGQNGHLRRDCPHSICYNCSWDGHRSN---HCPKPKKCYNCGETGHL 109
Query: 60 ----SDNDDQLLFCDDCDRGYH 77
+ + DQ C DC+ H
Sbjct: 110 SRDCNPSKDQQKSCFDCNSTRH 131
>gnl|CDD|153348 cd07664, BAR_SNX2, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexin 2. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions. Sorting nexins (SNXs)
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. SNX2 is a component of the retromer
complex, a membrane coat multimeric complex required for
endosomal retrieval of lysosomal hydrolase receptors to
the Golgi. The retromer consists of a cargo-recognition
subcomplex and a subcomplex formed by a dimer of sorting
nexins (SNX1 and/or SNX2), which ensures effcient cargo
sorting by facilitating proper membrane localization of
the cargo-recognition subcomplex. BAR domains form
dimers that bind to membranes, induce membrane bending
and curvature, and may also be involved in
protein-protein interactions.
Length = 234
Score = 27.7 bits (61), Expect = 3.5
Identities = 16/61 (26%), Positives = 31/61 (50%)
Query: 121 AETLEKLRKVEGRIACDEDLKLSDTLRYYMRDSDAAKRLLYRRLRCLADYENANRNLERA 180
AE EK+ ++ A + S+ L Y+R A K + +R++C +++A L++
Sbjct: 86 AEVEEKIDQLHQDQAFADFYLFSELLGDYIRLIAAVKGVFDQRMKCWQKWQDAQVTLQKK 145
Query: 181 R 181
R
Sbjct: 146 R 146
>gnl|CDD|150723 pfam10081, DUF2319, Predicted membrane protein (DUF2319). Members
of this family of hypothetical bacterial proteins have
no known function.
Length = 534
Score = 27.7 bits (62), Expect = 4.9
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 4 PTQAEKSGQPEDLVSCSDCGRSG 26
PT+ E+SG P LV GR G
Sbjct: 199 PTEPERSGSPASLVDWESLGRQG 221
>gnl|CDD|216249 pfam01025, GrpE, GrpE.
Length = 165
Score = 26.8 bits (60), Expect = 5.3
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 156 AKRLLYRRLRCLADYENANRNLERARTKNKD 186
+ L R LR LA++EN + ER R + K
Sbjct: 27 IEELKDRLLRLLAEFENYRKRTEREREEAKK 57
>gnl|CDD|225853 COG3316, COG3316, Transposase and inactivated derivatives [DNA
replication, recombination, and repair].
Length = 215
Score = 27.1 bits (60), Expect = 5.6
Identities = 13/56 (23%), Positives = 20/56 (35%), Gaps = 10/56 (17%)
Query: 110 RTVLKIGGFLPAETLEKLRKVEGRIACDEDLKLSDTLRYYMRDSDAAKRLLYRRLR 165
T +K+ G + A D D D R++ AAK L + L+
Sbjct: 77 ETYIKVNG----------KWHYLYRAIDADGLTLDVWLSKRRNALAAKAFLKKLLK 122
>gnl|CDD|129416 TIGR00316, cdhC, CO dehydrogenase/CO-methylating acetyl-CoA
synthase complex, beta subunit. Nomenclature follows
the description for Methanosarcina thermophila. The
CO-methylating acetyl-CoA synthase is considered the
defining enzyme of the Wood-Ljungdahl pathway, used for
acetate catabolism by sulfate reducing bacteria but for
acetate biosynthesis by acetogenic bacteria such as
oorella thermoacetica (f. Clostridium thermoaceticum)
[Energy metabolism, Chemoautotrophy].
Length = 458
Score = 27.1 bits (60), Expect = 5.6
Identities = 11/42 (26%), Positives = 24/42 (57%), Gaps = 5/42 (11%)
Query: 118 FLPAETLEKLRK-----VEGRIACDEDLKLSDTLRYYMRDSD 154
++P E E+++ + +IA +ED K +D LR ++++
Sbjct: 351 WMPKELKERVKDAIPEDLRDKIATEEDAKTTDELRKFLKEKG 392
>gnl|CDD|150335 pfam09634, DUF2025, Protein of unknown function (DUF2025). This
protein is produced from gene PA1123 in Pseudomonas. It
contains three alpha helices and six beta strands and is
thought to be monomeric. It appears to be present in the
biofilm layer and may be a lipoprotein.
Length = 106
Score = 26.0 bits (57), Expect = 6.3
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 137 DEDLKLSDTLRYYMRDSDAAKRLLYRRLR 165
D+ L + + LR Y+R SD + R LR
Sbjct: 78 DDRLNIGEPLRVYLRRSDLPEITAQRSLR 106
>gnl|CDD|219497 pfam07649, C1_3, C1-like domain. This short domain is rich in
cysteines and histidines. The pattern of conservation
is similar to that found in pfam00130.
Length = 30
Score = 24.2 bits (53), Expect = 6.4
Identities = 10/29 (34%), Positives = 13/29 (44%)
Query: 52 KCCSVCGTSDNDDQLLFCDDCDRGYHMYC 80
K C+ CG + D C +CD H C
Sbjct: 1 KTCNACGLPIDGDPFYSCSECDFVLHEDC 29
>gnl|CDD|220161 pfam09273, Rubis-subs-bind, Rubisco LSMT substrate-binding.
Members of this family adopt a multihelical structure,
with an irregular array of long and short alpha-helices.
They allow binding of the protein to substrate, such as
the N-terminal tails of histones H3 and H4 and the large
subunit of the Rubisco holoenzyme complex.
Length = 128
Score = 26.2 bits (58), Expect = 8.1
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 94 SCQLCLKEFHRKIEQGRTVLKIGGFLP-AETLEKLRKVEGRI 134
C+L L E+ +E+ +LK G +LR E RI
Sbjct: 86 LCKLLLSEYPTTLEEDEALLKKGNLSEQLRLAVRLRLGEKRI 127
>gnl|CDD|205270 pfam13089, PP_kinase_N, Polyphosphate kinase N-terminal domain.
Polyphosphate kinase (Ppk) catalyzes the formation of
polyphosphate from ATP, with chain lengths of up to a
thousand or more orthophosphate molecules.
Length = 109
Score = 25.5 bits (57), Expect = 9.0
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 103 HRKIEQGRTVLKIGGFLPAETLEKLRK 129
R+IE G T G P+E LE + +
Sbjct: 53 KRQIEAGVTKRSPDGLTPSEQLEAISE 79
>gnl|CDD|238252 cd00446, GrpE, GrpE is the adenine nucleotide exchange factor of
DnaK (Hsp70)-type ATPases. The GrpE dimer binds to the
ATPase domain of Hsp70 catalyzing the dissociation of
ADP, which enables rebinding of ATP, one step in the
Hsp70 reaction cycle in protein folding. In eukaryotes,
only the mitochondrial Hsp70, not the cytosolic form, is
GrpE dependent.
Length = 137
Score = 25.9 bits (58), Expect = 9.7
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 162 RRLRCLADYENANRNLERARTKNKD 186
+ LR LA++EN + ER R + +
Sbjct: 7 KLLRALAEFENYRKRTEREREEARK 31
>gnl|CDD|184136 PRK13552, frdB, fumarate reductase iron-sulfur subunit;
Provisional.
Length = 239
Score = 26.4 bits (59), Expect = 9.8
Identities = 9/13 (69%), Positives = 10/13 (76%), Gaps = 1/13 (7%)
Query: 48 CIECKCC-SVCGT 59
CIEC CC + CGT
Sbjct: 151 CIECGCCVAACGT 163
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
0.323 0.137 0.447
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,355,171
Number of extensions: 833015
Number of successful extensions: 954
Number of sequences better than 10.0: 1
Number of HSP's gapped: 948
Number of HSP's successfully gapped: 63
Length of query: 190
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 99
Effective length of database: 6,901,388
Effective search space: 683237412
Effective search space used: 683237412
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 (22.0 bits)
S2: 56 (25.2 bits)