RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5492
(361 letters)
>gnl|CDD|153339 cd07655, F-BAR_PACSIN, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Protein kinase C and
Casein kinase Substrate in Neurons (PACSIN) proteins.
F-BAR domains are dimerization modules that bind and
bend membranes and are found in proteins involved in
membrane dynamics and actin reorganization. Protein
kinase C and Casein kinase Substrate in Neurons (PACSIN)
proteins, also called Synaptic dynamin-associated
proteins (Syndapins), act as regulators of cytoskeletal
and membrane dynamics. They bind both dynamin and
Wiskott-Aldrich syndrome protein (WASP), and may provide
direct links between the actin cytoskeletal machinery
through WASP and dynamin-dependent endocytosis.
Vetebrates harbor three isoforms with distinct
expression patterns and specific functions. PACSINs
contain an N-terminal F-BAR domain and a C-terminal SH3
domain. F-BAR domains form banana-shaped dimers with a
positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules.
Length = 258
Score = 284 bits (728), Expect = 2e-95
Identities = 132/244 (54%), Positives = 160/244 (65%), Gaps = 38/244 (15%)
Query: 44 FWEPGNYKRTTKRIEDGYKLCNDLIALIQERADIEKAYAKSLKGWNKKWNELIEK----- 98
FWE GNYKRT KRIEDG+KLC+DL+ ++QERA+IEKAYAK LK W KKW +LIEK
Sbjct: 1 FWEVGNYKRTVKRIEDGHKLCDDLMKMVQERAEIEKAYAKKLKEWAKKWRDLIEKGPEYG 60
Query: 99 ------------VMRTC--------------------WQKDTYHKTVL-HIKERKEMEDA 125
R WQK+ YHK+++ KE KE ED
Sbjct: 61 TLETAWKGLLSEAERLSELHLSIRDKLLNDVVEEVKTWQKENYHKSMMGGFKETKEAEDG 120
Query: 126 FKKAQKPWCKLLTKVNKTKNDYHVACKAERSASNQERNASADSSLSMDQLKKMQDRVQKA 185
F KAQKPW KLL KV K K YH ACKAE+SA QE NA +D+SLS DQ+KK+QD+V+K
Sbjct: 121 FAKAQKPWAKLLKKVEKAKKAYHAACKAEKSAQKQENNAKSDTSLSPDQVKKLQDKVEKC 180
Query: 186 KEEVQKAKEKYELALQELNSYNPKYMEDMSVVFDKCQEMETTRLQFFKDSLFSIHKCLNI 245
K+EV K K+KYE AL++LN YNP+YMEDM VFDKCQE E RL FFK+ L S H+ L++
Sbjct: 181 KQEVSKTKDKYEKALEDLNKYNPRYMEDMEQVFDKCQEFEEKRLDFFKEILLSYHRHLDL 240
Query: 246 SQDP 249
S +P
Sbjct: 241 STNP 244
Score = 40.8 bits (96), Expect = 6e-04
Identities = 20/39 (51%), Positives = 23/39 (58%), Gaps = 7/39 (17%)
Query: 253 HIKERKEMEDAFKKAQKPWCKTVLHIKERKEMEDAFKKA 291
KE KE ED F KAQKPW K + K++E A KKA
Sbjct: 110 GFKETKEAEDGFAKAQKPWAKLL------KKVEKA-KKA 141
Score = 38.8 bits (91), Expect = 0.002
Identities = 13/23 (56%), Positives = 14/23 (60%)
Query: 273 KTVLHIKERKEMEDAFKKAQKPW 295
+ KE KE ED F KAQKPW
Sbjct: 106 SMMGGFKETKEAEDGFAKAQKPW 128
>gnl|CDD|153365 cd07681, F-BAR_PACSIN3, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Protein kinase C and
Casein kinase Substrate in Neurons 3 (PACSIN3). F-BAR
domains are dimerization modules that bind and bend
membranes and are found in proteins involved in membrane
dynamics and actin reorganization. Protein kinase C and
Casein kinase Substrate in Neurons (PACSIN) proteins,
also called Synaptic dynamin-associated proteins
(Syndapins), act as regulators of cytoskeletal and
membrane dynamics. Vetebrates harbor three isoforms with
distinct expression patterns and specific functions.
PACSIN 3 or Syndapin III is expressed ubiquitously and
regulates glucose uptake in adipocytes through its role
in GLUT1 trafficking. It also modulates the subcellular
localization and stimulus-specific function of the
cation channel TRPV4. PACSIN 3 contains an N-terminal
F-BAR domain and a C-terminal SH3 domain. F-BAR domains
form banana-shaped dimers with a positively-charged
concave surface that binds to negatively-charged lipid
membranes. They can induce membrane deformation in the
form of long tubules.
Length = 258
Score = 215 bits (549), Expect = 2e-68
Identities = 111/241 (46%), Positives = 149/241 (61%), Gaps = 38/241 (15%)
Query: 44 FWEPGNYKRTTKRIEDGYKLCNDLIALIQERADIEKAYAKSLKGWNKKWNELIEK----- 98
FWE GNY+RT KRIEDGY+LCNDL++ QERA IEK YA+ L W +KW ++EK
Sbjct: 1 FWEAGNYRRTVKRIEDGYRLCNDLVSCFQERAKIEKGYAQQLSDWARKWRGIVEKGPQYG 60
Query: 99 ---------------------VMRT-----------CWQKDTYHKTVLH-IKERKEMEDA 125
+R WQK+ +HK ++ +E KE E+
Sbjct: 61 TLEKAWHAFLTAAERLSEIHLELRENLVGEDSEKVRAWQKEAFHKQMIGGFRESKEAEEG 120
Query: 126 FKKAQKPWCKLLTKVNKTKNDYHVACKAERSASNQERNASADSSLSMDQLKKMQDRVQKA 185
F+KAQKPW K L +V +K YH A K ER+A +E +A ADS++S +QL+K+QDRV+K
Sbjct: 121 FRKAQKPWVKKLKEVESSKKGYHAARKDERTAQTRETHAKADSTVSQEQLRKLQDRVEKC 180
Query: 186 KEEVQKAKEKYELALQELNSYNPKYMEDMSVVFDKCQEMETTRLQFFKDSLFSIHKCLNI 245
+E +KAKE+YE AL+ELN YNP+YMEDM F+ CQE E RL FFK+ L +H+ L++
Sbjct: 181 TQEAEKAKEQYEKALEELNRYNPRYMEDMEQAFEICQEAERKRLCFFKEMLLDLHQHLDL 240
Query: 246 S 246
S
Sbjct: 241 S 241
Score = 34.1 bits (78), Expect = 0.086
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 6/62 (9%)
Query: 240 HKCLNISQDPTVLHIKERKEMEDAFKKAQKPWCKTVLH------IKERKEMEDAFKKAQK 293
H L ++ + +H++ R+ + + + W K H +E KE E+ F+KAQK
Sbjct: 67 HAFLTAAERLSEIHLELRENLVGEDSEKVRAWQKEAFHKQMIGGFRESKEAEEGFRKAQK 126
Query: 294 PW 295
PW
Sbjct: 127 PW 128
Score = 33.4 bits (76), Expect = 0.12
Identities = 15/39 (38%), Positives = 25/39 (64%)
Query: 255 KERKEMEDAFKKAQKPWCKTVLHIKERKEMEDAFKKAQK 293
+E KE E+ F+KAQKPW K + ++ K+ A +K ++
Sbjct: 112 RESKEAEEGFRKAQKPWVKKLKEVESSKKGYHAARKDER 150
>gnl|CDD|153364 cd07680, F-BAR_PACSIN1, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Protein kinase C and
Casein kinase Substrate in Neurons 1 (PACSIN1). F-BAR
domains are dimerization modules that bind and bend
membranes and are found in proteins involved in membrane
dynamics and actin reorganization. Protein kinase C and
Casein kinase Substrate in Neurons (PACSIN) proteins,
also called Synaptic dynamin-associated proteins
(Syndapins), act as regulators of cytoskeletal and
membrane dynamics. Vetebrates harbor three isoforms with
distinct expression patterns and specific functions.
PACSIN 1 or Syndapin I is expressed specifically in the
brain and is localized in neurites and synaptic boutons.
It binds the brain-specific proteins dynamin I,
synaptojanin, synapsin I, and neural Wiskott-Aldrich
syndrome protein (nWASP), and functions as a link
between the cytoskeletal machinery and synaptic vesicle
endocytosis. PACSIN 1 interacts with huntingtin and may
be implicated in the neuropathology of Huntington's
disease. It contains an N-terminal F-BAR domain and a
C-terminal SH3 domain. F-BAR domains form banana-shaped
dimers with a positively-charged concave surface that
binds to negatively-charged lipid membranes. They can
induce membrane deformation in the form of long tubules.
Length = 258
Score = 199 bits (508), Expect = 2e-62
Identities = 106/254 (41%), Positives = 148/254 (58%), Gaps = 38/254 (14%)
Query: 44 FWEPGNYKRTTKRIEDGYKLCNDLIALIQERADIEKAYAKSLKGWNKKWNELIEK----- 98
FWE GNYKRT KRI+DG++LCNDL+ +QERA IEKAY + L W K+W +LIEK
Sbjct: 1 FWEVGNYKRTVKRIDDGHRLCNDLMNCVQERAKIEKAYGQQLTDWAKRWRQLIEKGPQYG 60
Query: 99 --------VMRTC------------------------WQKDTYHKTVLH-IKERKEMEDA 125
+M WQKD YHK ++ KE KE ED
Sbjct: 61 SLERAWGAIMTEADKVSELHQEVKNNLLNEDLEKVKNWQKDAYHKQIMGGFKETKEAEDG 120
Query: 126 FKKAQKPWCKLLTKVNKTKNDYHVACKAERSASNQERNASADSSLSMDQLKKMQDRVQKA 185
F+KAQKPW K + ++ K YH+ACK E+ A +E N+ A+ S++ +Q KK+QD+V K
Sbjct: 121 FRKAQKPWAKKMKELEAAKKAYHLACKEEKLAMTREANSKAEQSVTPEQQKKLQDKVDKC 180
Query: 186 KEEVQKAKEKYELALQELNSYNPKYMEDMSVVFDKCQEMETTRLQFFKDSLFSIHKCLNI 245
K++VQK +EKYE L ++ P+YME+M VF++CQ+ E RL F K+ L I + LN+
Sbjct: 181 KQDVQKTQEKYEKVLDDVGKTTPQYMENMEQVFEQCQQFEEKRLVFLKEVLLDIKRHLNL 240
Query: 246 SQDPTVLHIKERKE 259
++ + H+ E
Sbjct: 241 AESSSYAHVYRELE 254
Score = 32.3 bits (73), Expect = 0.29
Identities = 19/35 (54%), Positives = 22/35 (62%), Gaps = 6/35 (17%)
Query: 255 KERKEMEDAFKKAQKPWCKTVLHIKERKEMEDAFK 289
KE KE ED F+KAQKPW K + KE+E A K
Sbjct: 112 KETKEAEDGFRKAQKPWAKKM------KELEAAKK 140
>gnl|CDD|153363 cd07679, F-BAR_PACSIN2, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Protein kinase C and
Casein kinase Substrate in Neurons 2 (PACSIN2). F-BAR
domains are dimerization modules that bind and bend
membranes and are found in proteins involved in membrane
dynamics and actin reorganization. Protein kinase C and
Casein kinase Substrate in Neurons (PACSIN) proteins,
also called Synaptic dynamin-associated proteins
(Syndapins), act as regulators of cytoskeletal and
membrane dynamics. Vetebrates harbor three isoforms with
distinct expression patterns and specific functions.
PACSIN 2 or Syndapin II is expressed ubiquitously and is
involved in the regulation of tubulin polymerization. It
associates with Golgi membranes and forms a complex with
dynamin II which is crucial in promoting vesicle
formation from the trans-Golgi network. PACSIN 2
contains an N-terminal F-BAR domain and a C-terminal SH3
domain. F-BAR domains form banana-shaped dimers with a
positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules.
Length = 258
Score = 189 bits (481), Expect = 3e-58
Identities = 106/241 (43%), Positives = 149/241 (61%), Gaps = 38/241 (15%)
Query: 44 FWEPGNYKRTTKRIEDGYKLCNDLIALIQERADIEKAYAKSLKGWNKKWNELIEK----- 98
FWE GNYKRT KRI+DG++LCNDL+ + ERA IEK YA+ L W K+W +L+EK
Sbjct: 1 FWEVGNYKRTVKRIDDGHRLCNDLMNCLHERARIEKVYAQQLTEWAKRWRQLVEKGPQYG 60
Query: 99 -VMRTC-------------------------------WQKDTYHKTVLH-IKERKEMEDA 125
V + WQK+ +HK ++ KE KE ED
Sbjct: 61 TVEKAWCALMSEAEKVSELHLEVKASLMNEDFEKIKNWQKEAFHKQMMGGFKETKEAEDG 120
Query: 126 FKKAQKPWCKLLTKVNKTKNDYHVACKAERSASNQERNASADSSLSMDQLKKMQDRVQKA 185
F+KAQKPW K L +V K YH ACK E+ A+++E N+ AD +L+ +QLKK+QD+V+K
Sbjct: 121 FRKAQKPWAKKLKEVEAAKKAYHTACKEEKLATSREANSKADPALNPEQLKKLQDKVEKC 180
Query: 186 KEEVQKAKEKYELALQELNSYNPKYMEDMSVVFDKCQEMETTRLQFFKDSLFSIHKCLNI 245
K++V K KEKYE +L+EL+ P+YME+M VF++CQ+ E RL+FF++ L + K L++
Sbjct: 181 KQDVLKTKEKYEKSLKELDQTTPQYMENMEQVFEQCQQFEEKRLRFFREVLLEVQKHLDL 240
Query: 246 S 246
S
Sbjct: 241 S 241
Score = 34.3 bits (78), Expect = 0.081
Identities = 17/39 (43%), Positives = 23/39 (58%)
Query: 255 KERKEMEDAFKKAQKPWCKTVLHIKERKEMEDAFKKAQK 293
KE KE ED F+KAQKPW K + ++ K+ K +K
Sbjct: 112 KETKEAEDGFRKAQKPWAKKLKEVEAAKKAYHTACKEEK 150
>gnl|CDD|216021 pfam00611, FCH, Fes/CIP4, and EFC/F-BAR homology domain.
Alignment extended from. Highly alpha-helical. The
cytosolic endocytic adaptor proteins in fungi carry
this domain at the N-terminus; several of these have
been referred to as muniscin proteins. These N-terminal
BAR, N-BAR, and EFC/F-BAR domains are found in proteins
that regulate membrane trafficking events by inducing
membrane tubulation. The domain dimerises into a curved
structure that binds to liposomes and either senses or
induces the curvature of the membrane bilayer to cause
biophysical changes to the shape of the bilayer; it
also thereby recruits other trafficking factors, such
as the GTPase dynamin. Most EFC/F-BAR domain-family
members localise to actin-rich structures.
Length = 91
Score = 57.7 bits (140), Expect = 8e-11
Identities = 24/59 (40%), Positives = 35/59 (59%), Gaps = 2/59 (3%)
Query: 42 DSFWEPGN--YKRTTKRIEDGYKLCNDLIALIQERADIEKAYAKSLKGWNKKWNELIEK 98
DSFW + +K KR++ G KL +L ++ERA+IEK YAK L+ KK+ + E
Sbjct: 1 DSFWSELDDGFKVLLKRLKQGIKLLEELAKFLRERAEIEKEYAKKLRKLAKKYLKKKEG 59
>gnl|CDD|153335 cd07651, F-BAR_PombeCdc15_like, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Schizosaccharomyces pombe
Cdc15, and similar proteins. F-BAR domains are
dimerization modules that bind and bend membranes and
are found in proteins involved in membrane dynamics and
actin reorganization. This subfamily is composed of
Schizosaccharomyces pombe Cdc15 and Imp2, and similar
proteins. These proteins contain an N-terminal F-BAR
domain and a C-terminal SH3 domain. S. pombe Cdc15 and
Imp2 play both distinct and overlapping roles in the
maintenance and strengthening of the contractile ring at
the division site, which is required in cell division.
Cdc15 is a component of the actomyosin ring and is
required in normal cytokinesis. Imp2 colocalizes with
the medial ring during septation and is required for
normal septation. F-BAR domains form banana-shaped
dimers with a positively-charged concave surface that
binds to negatively-charged lipid membranes. They can
induce membrane deformation in the form of long tubules.
Length = 236
Score = 57.7 bits (140), Expect = 1e-09
Identities = 45/219 (20%), Positives = 88/219 (40%), Gaps = 36/219 (16%)
Query: 56 RIEDGYKLCNDLIALIQERADIEKAYAKSLKGWNKK------------------------ 91
RI+D + +L + +ERA IE+ YAK L+ ++K
Sbjct: 13 RIKDSLRTLEELRSFYKERASIEEEYAKRLEKLSRKSLGGSEEGGLKNSLDTLRLETESM 72
Query: 92 --WNELIEKVMRTCWQKDTYHKTVLHIKERKEMEDAFKKAQKPWCKLLTKVNKTKNDYHV 149
+ K +R ++ + ++RK+++ +K K + K + Y
Sbjct: 73 AKSHLKFAKQIRQDLEEKLAAFASSYTQKRKKIQSHMEKLLKKKQDQEKYLEKAREKYEA 132
Query: 150 ACKAERSASNQERNASADSSLSMDQ-LKKMQDRVQKAKEEVQKAKEKYELALQELNSYNP 208
C S + Q S L+ + L+K ++ KA+ + ++ Y+ A++ L N
Sbjct: 133 DCSKINSYTLQ-------SQLTWGKELEKNNAKLNKAQSSINSSRRDYQNAVKALRELNE 185
Query: 209 KYMEDMSVVFDKCQEMETTRLQFFKDSLFSIHKCLNISQ 247
+ + D Q++E R+QF K + ++ NIS
Sbjct: 186 IWNREWKAALDDFQDLEEERIQFLKSNCWTF--ANNIST 222
>gnl|CDD|153331 cd07647, F-BAR_PSTPIP, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Proline-Serine-Threonine
Phosphatase-Interacting Proteins. F-BAR domains are
dimerization modules that bind and bend membranes and
are found in proteins involved in membrane dynamics and
actin reorganization. Vetebrates contain two
Proline-Serine-Threonine Phosphatase-Interacting
Proteins (PSTPIPs), PSTPIP1 and PSTPIP2. PSTPIPs are
mainly expressed in hematopoietic cells and are involved
in the regulation of cell adhesion and motility.
Mutations in PSTPIPs have been shown to cause
autoinflammatory disorders. PSTPIP1 contains an
N-terminal F-BAR domain, PEST motifs, and a C-terminal
SH3 domain, while PSTPIP2 contains only the N-terminal
F-BAR domain. F-BAR domains form banana-shaped dimers
with a positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules.
Length = 239
Score = 54.4 bits (131), Expect = 2e-08
Identities = 45/217 (20%), Positives = 90/217 (41%), Gaps = 37/217 (17%)
Query: 50 YKRTTKRIEDGYKLCNDLIALIQERADIEKAYAKSL-KGWNKKWNELIEKVMRTCWQKDT 108
+ +R+++G K+C +L +++RA E+ Y K+L K +++ W D+
Sbjct: 7 FDTLLQRLKEGKKMCKELEDFLKQRAKAEEDYGKALLKLSKSAGPGDEIGTLKSSW--DS 64
Query: 109 YHKTVLHI--------------------------KERKEMEDAFKKAQKPWCKLLTKVNK 142
K ++ +ERK+ ED K++QK +L K K
Sbjct: 65 LRKETENVANAHIQLAQSLREEAEKLEEFREKQKEERKKTEDIMKRSQKNKKELYKKTMK 124
Query: 143 TKNDYHVACKAERSASNQERNASADSSLSMDQLK---KMQDRVQKAKEEVQKAKEKYELA 199
K Y C+ + A + + S S Q K K++ + + K ++A Y+ +
Sbjct: 125 AKKSYEQKCREKDKAEQ-----AYEKSSSGAQPKEAEKLKKKAAQCKTSAEEADSAYKSS 179
Query: 200 LQELNSYNPKYMEDMSVVFDKCQEMETTRLQFFKDSL 236
+ L ++ + + Q ME R++F +++L
Sbjct: 180 IGCLEDARVEWESEHATACQVFQNMEEERIKFLRNAL 216
>gnl|CDD|153337 cd07653, F-BAR_CIP4-like, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Cdc42-Interacting Protein
4 and similar proteins. F-BAR domains are dimerization
modules that bind and bend membranes and are found in
proteins involved in membrane dynamics and actin
reorganization. This subfamily is composed of
Cdc42-Interacting Protein 4 (CIP4), Formin Binding
Protein 17 (FBP17), FormiN Binding Protein 1-Like
(FNBP1L), and similar proteins. CIP4 and FNBP1L are
Cdc42 effectors that bind Wiskott-Aldrich syndrome
protein (WASP) and function in endocytosis. CIP4 and
FBP17 bind to the Fas ligand and may be implicated in
the inflammatory response. CIP4 may also play a role in
phagocytosis. Members of this subfamily typically
contain an N-terminal F-BAR domain and a C-terminal SH3
domain. In addition, some members such as FNBP1L contain
a central Cdc42-binding HR1 domain. F-BAR domains form
banana-shaped dimers with a positively-charged concave
surface that binds to negatively-charged lipid
membranes. They can induce membrane deformation in the
form of long tubules.
Length = 251
Score = 53.4 bits (129), Expect = 4e-08
Identities = 49/209 (23%), Positives = 85/209 (40%), Gaps = 34/209 (16%)
Query: 55 KRIEDGYKLCNDLIALIQERADIEKAYAKSLKGWNKKW---------------------- 92
K + G ++ERA IE+ YAK L+ KK+
Sbjct: 12 KHTQKGIDFLERYGKFVKERAAIEQEYAKKLRKLVKKYLPKKKEEDEYSFSSVKAFRSIL 71
Query: 93 ---------NELIEKVMRTCWQKDTYHKTVLHIKERKEMEDAFKKAQKPWCKLLTKVNKT 143
+ELI + + + K+ +ERK+ K Q+ + ++ K+
Sbjct: 72 NEVNDIAGQHELIAENLNSNVCKELKTLISELRQERKKHLSEGSKLQQKLESSIKQLEKS 131
Query: 144 KNDYHVACK-AERSASNQERNASADSSLSMDQLKKMQDRVQKAKEEVQKAKEKYELALQE 202
K Y A K AE++ E+ A AD +L+ ++K + + ++AK +Y LQ+
Sbjct: 132 KKAYEKAFKEAEKAKQKYEK-ADADMNLTKADVEKAKANANLKTQAAEEAKNEYAAQLQK 190
Query: 203 LNSY-NPKYMEDMSVVFDKCQEMETTRLQ 230
N Y D+ +FDK QE++ R+
Sbjct: 191 FNKEQRQHYSTDLPQIFDKLQELDEKRIN 219
>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 = 45.0 bits (107), Expect = 2e-06
Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 42 DSFWEPG--NYKRTTKRIEDGYKLCNDLIALIQERADIEKAYAKSLKGWNKKW 92
FW ++ R+++G +L DL ++ERA IE+ YAK L+ +KK
Sbjct: 1 MGFWSELDDGFEALLSRLKNGLRLLEDLKKFMRERAKIEEEYAKKLQKLSKKL 53
>gnl|CDD|153294 cd07610, FCH_F-BAR, The Extended FES-CIP4 Homology (FCH) or F-BAR
(FCH and Bin/Amphiphysin/Rvs) domain, a dimerization
module that binds and bends membranes. F-BAR domains
are dimerization modules that bind and bend membranes
and are found in proteins involved in membrane dynamics
and actin reorganization. F-BAR domain containing
proteins, also known as Pombe Cdc15 homology (PCH)
family proteins, include Fes and Fer tyrosine kinases,
PACSINs/Syndapins, FCHO, PSTPIP, CIP4-like proteins and
srGAPs. Many members also contain an SH3 domain and play
roles in endocytosis. F-BAR domains form banana-shaped
dimers with a positively-charged concave surface that
binds to negatively-charged lipid membranes. They can
induce membrane deformation in the form of long tubules.
These tubules have diameters larger than those observed
with N-BARs. The F-BAR domains of some members such as
NOSTRIN and Rgd1 are important for the subcellular
localization of the protein.
Length = 191
Score = 46.2 bits (110), Expect = 5e-06
Identities = 46/187 (24%), Positives = 77/187 (41%), Gaps = 20/187 (10%)
Query: 50 YKRTTKRIEDGYKLCNDLIALIQERADIEKAYAKSLKGWNKKWNELIEKVMRTCWQKDTY 109
++ KR E G L DL +++RA IE+ YAK+L+ KK+++ E +
Sbjct: 2 FELLEKRTELGLDLLKDLREFLKKRAAIEEEYAKNLQKLAKKFSKKPESGKTSLGT---- 57
Query: 110 HKTVLHIKERKEMEDAFKKAQKPWCKLLTKVNKTKNDYHVACKAERSASNQERNASADSS 169
R+E E A ++ KL + + + + A +E
Sbjct: 58 ----SWNSLREETESAATVHEELSEKLSQLIRE---PLEKVKEDKEQARKKELAEGEKLK 110
Query: 170 LSMDQLKKMQDRVQKAKEEVQKAKEKYELALQELNSYNPKYMEDMSVVFDKCQEMETTRL 229
KK+Q+ K + KA E+Y +++LN +Y E+ QE E RL
Sbjct: 111 ------KKLQELWAKLAK---KADEEYREQVEKLNPAQSEYEEEKLNKIQAEQEREEERL 161
Query: 230 QFFKDSL 236
+ KD+L
Sbjct: 162 EILKDNL 168
>gnl|CDD|153342 cd07658, F-BAR_NOSTRIN, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Nitric Oxide Synthase
TRaffic INducer (NOSTRIN). F-BAR domains are
dimerization modules that bind and bend membranes and
are found in proteins involved in membrane dynamics and
actin reorganization. Nitric Oxide Synthase TRaffic
INducer (NOSTRIN) is expressed in endothelial and
epithelial cells and is involved in the regulation,
trafficking and targeting of endothelial NOS (eNOS).
NOSTRIN facilitates the endocytosis of eNOS by
coordinating the functions of dynamin and the
Wiskott-Aldrich syndrome protein (WASP). Increased
expression of NOSTRIN may be correlated to preeclampsia.
NOSTRIN contains an N-terminal F-BAR domain and a
C-terminal SH3 domain. F-BAR domains form banana-shaped
dimers with a positively-charged concave surface that
binds to negatively-charged lipid membranes. They can
induce membrane deformation in the form of long tubules.
The F-BAR domain of NOSTRIN is necessary and sufficient
for its membrane association and is responsible for its
subcellular localization.
Length = 239
Score = 45.8 bits (109), Expect = 1e-05
Identities = 47/239 (19%), Positives = 87/239 (36%), Gaps = 41/239 (17%)
Query: 44 FWEPGNYKRTTKRIEDGYKLCNDLIALIQERADIEKAYAKSLKGWNKKWNELIEKV---M 100
F ++ + ++ G C +L ++QERA++E YAK L + K ++ + V +
Sbjct: 1 FMGQKGFEELRRYVKQGGDFCKELATVLQERAELELNYAKGLSKLSGKLSKASKSVSGTL 60
Query: 101 RTCWQK--------DTYH---------------KTVL--HIKERKEMEDAFKKAQKPWCK 135
+ W H + VL K RK +E+ KA K
Sbjct: 61 SSAWTCVAEEMESEADIHRNLGSALTEEAIKPLRQVLDEQHKTRKPVENEVDKAAKLLTD 120
Query: 136 LLTKVNKTKNDYHVACKA-ERSASNQERNASADSSLSMDQLK------------KMQDRV 182
++ K K H + E+ E N + + M K++ +
Sbjct: 121 WRSEQIKVKKKLHGLARENEKLQDQVEDNKQSCTKQKMLNKLKKSAEVQDKEDEKLEAKR 180
Query: 183 QKAKEEVQKAKEKYELALQELNSYNPKYMEDMSVVFDKCQEMETTRLQFFKDSLFSIHK 241
+K +E KA+ +Y L ++ + ++ + +E RLQ K SL +
Sbjct: 181 KKGEESRLKAENEYYTCCVRLERLRLEWESALRKGLNQYESLEEERLQHLKHSLSQYLR 239
>gnl|CDD|153355 cd07671, F-BAR_PSTPIP1, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Proline-Serine-Threonine
Phosphatase-Interacting Protein 1. F-BAR domains are
dimerization modules that bind and bend membranes and
are found in proteins involved in membrane dynamics and
actin reorganization. Proline-Serine-Threonine
Phosphatase-Interacting Protein 1 (PSTPIP1), also known
as CD2 Binding Protein 1 (CD2BP1), is mainly expressed
in hematopoietic cells. It is a binding partner of the
cell surface receptor CD2 and PTP-PEST, a tyrosine
phosphatase which functions in cell motility and Rac1
regulation. It also plays a role in the activation of
the Wiskott-Aldrich syndrome protein (WASP), which
couples actin rearrangement and T cell activation.
Mutations in the gene encoding PSTPIP1 cause the
autoinflammatory disorder known as PAPA (pyogenic
sterile arthritis, pyoderma gangrenosum, and acne)
syndrome. PSTPIP1 contains an N-terminal F-BAR domain,
PEST motifs, and a C-terminal SH3 domain. F-BAR domains
form banana-shaped dimers with a positively-charged
concave surface that binds to negatively-charged lipid
membranes. They can induce membrane deformation in the
form of long tubules.
Length = 242
Score = 38.0 bits (88), Expect = 0.004
Identities = 44/216 (20%), Positives = 91/216 (42%), Gaps = 33/216 (15%)
Query: 50 YKRTTKRIEDGYKLCNDLIALIQERADIEKAYAKSLKGWNKKWNELIEKVMRTCW----- 104
Y+ +R+ DG K+C D+ L+++RA E+ Y K L +K E + T
Sbjct: 7 YEILLQRLLDGRKMCKDVEELLKQRAQAEERYGKELVQIARKAGGQTE--INTLKASFDQ 64
Query: 105 -QKDTYHKTVLHIK---------------------ERKEMEDAFKKAQKPWCKLLTKVNK 142
++ + HI+ +RK+ E ++ QK L K +
Sbjct: 65 LKQQIENIGNSHIQLAGMLREELKSLEEFRERQKEQRKKYEAVMERVQKSKVSLYKKTME 124
Query: 143 TKNDYHVACKAERSASNQERNASADSSL-SMDQLKKMQDRVQKAKEEVQKAKEKYELALQ 201
+K Y C R A E+ SS + Q +K Q++ ++ ++ +A+ Y+ ++
Sbjct: 125 SKKTYEQRC---READEAEQTFERSSSTGNPKQSEKSQNKAKQCRDAATEAERVYKQNIE 181
Query: 202 ELNSYNPKYMEDMSVVFDKCQEMETTRLQFFKDSLF 237
+L+ ++ + + + Q E R+ +++L+
Sbjct: 182 QLDKARTEWETEHILTCEVFQLQEDDRITILRNALW 217
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 37.9 bits (89), Expect = 0.008
Identities = 26/147 (17%), Positives = 59/147 (40%), Gaps = 37/147 (25%)
Query: 119 RKEMEDAFKKAQKPWCKLLTKVNKTKNDYHVACKAERSASNQERNASADSSLSMDQLKKM 178
+E+E ++A+ LL + K K + E+ QE D+L +
Sbjct: 529 ERELEQKAEEAEA----LLKEAEKLKEEL-----EEKKEKLQEE---------EDKLLEE 570
Query: 179 QDRVQKAKEEVQKAKEKYELALQELNSYNPKYMEDMSVVFDKCQEMETTRLQFFKDSLFS 238
+ ++A++ +++AK++ + ++EL + ++ K E+
Sbjct: 571 AE--KEAQQAIKEAKKEADEIIKEL-----RQLQKGGYASVKAHELI------------E 611
Query: 239 IHKCLNISQDPTVLHIKERKEMEDAFK 265
K LN + + K++KE ++ K
Sbjct: 612 ARKRLNKANEKKEKKKKKQKEKQEELK 638
>gnl|CDD|227606 COG5281, COG5281, Phage-related minor tail protein [Function
unknown].
Length = 833
Score = 36.5 bits (84), Expect = 0.023
Identities = 26/171 (15%), Positives = 49/171 (28%), Gaps = 14/171 (8%)
Query: 48 GNYKRTTKRIEDGYKLCNDLIALIQER-ADIEKAYAKSLKGWNKKWNELIEKVMRTCWQK 106
G+ + +D A ++E +E A+ K W+ ++
Sbjct: 296 GDTAAAAAAAAEAAAAMDDRTARVKENMGTLETAWDALADAAKKMWDAVLGIGREDKQAA 355
Query: 107 DTYHKTVLHIKERKEMEDAFKKAQKPWCKLLTKVNKTKNDYHVACKAERSASNQERNASA 166
K A K A+ L K D + +A++Q N
Sbjct: 356 LLAAK-----------LAAEKLARVTAQGALNARLKLAQDDLTQAELNYAAADQAANQEG 404
Query: 167 DSSLSMDQL--KKMQDRVQKAKEEVQKAKEKYELALQELNSYNPKYMEDMS 215
+ D+ Q+ + + + EK +ELN K +
Sbjct: 405 ALNAREDEAEVLSTQEERRDILKNLLADAEKRTARQEELNKALAKAKILQA 455
>gnl|CDD|225087 COG2176, PolC, DNA polymerase III, alpha subunit (gram-positive
type) [DNA replication, recombination, and repair].
Length = 1444
Score = 34.6 bits (80), Expect = 0.089
Identities = 35/185 (18%), Positives = 66/185 (35%), Gaps = 13/185 (7%)
Query: 35 NMLIASSDSFWEPGNYKRTTKRIEDGYKLCNDLIALIQERADIEKAYAKSLKGWNKKWNE 94
L+A + E N T + I+ +K + +++ I K+ LK K N
Sbjct: 72 EQLVAKVEFDIEVRNVDITEQEIQTYFKKIIEQLSVKSP---IFKSLLNKLKLKVKGNNI 128
Query: 95 LIEKVMRTCWQKDTYHKTVLHIKERKEMEDAFKKAQKPWCKLLTKVNKTKNDYHVACKAE 154
LIE+V + + E++ + P + +VN + +
Sbjct: 129 LIEQV-------LNNPEFDHFKNKSPELQKKLQSFGFPQLLIEFEVNDISEEQEF--EKF 179
Query: 155 RSASNQERNASADSSLS-MDQLKKMQDRVQKAKEEVQKAKEKYELALQELNSYNPKYMED 213
A N+E +A +L +LK +V+K K K + + +E+ E+
Sbjct: 180 EEAINEEVEKAAQEALEAEKKLKAESPKVEKPKPLFDGQKGRKIKSTEEIKPLIKINEEE 239
Query: 214 MSVVF 218
V
Sbjct: 240 TRVKV 244
>gnl|CDD|237930 PRK15249, PRK15249, fimbrial chaperone protein StbB; Provisional.
Length = 253
Score = 32.8 bits (75), Expect = 0.19
Identities = 19/64 (29%), Positives = 27/64 (42%), Gaps = 3/64 (4%)
Query: 17 SCEGAQAVLGGMSHHSDENMLIA--SSDSFWEPGNYKRTTKRIEDGYKLCNDLIALIQER 74
S + G S++ D +M IA SS ++W PG + L ND A I E
Sbjct: 189 SLSNLNVKVNGASYNLDADM-IAPFSSQTWWLPGKRSLKSFSGTVTVTLVNDQGARISES 247
Query: 75 ADIE 78
D+
Sbjct: 248 YDVP 251
>gnl|CDD|153360 cd07676, F-BAR_FBP17, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Formin Binding Protein
17. F-BAR domains are dimerization modules that bind
and bend membranes and are found in proteins involved in
membrane dynamics and actin reorganization. Formin
Binding Protein 17 (FBP17), also called FormiN Binding
Protein 1 (FNBP1), is involved in dynamin-mediated
endocytosis. It is recruited to clathrin-coated pits
late in the endocytosis process and may play a role in
the invagination and scission steps. FBP17 binds in vivo
to tankyrase, a protein involved in telomere maintenance
and mitogen activated protein kinase (MAPK) signaling.
F-BAR domains form banana-shaped dimers with a
positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules.
Length = 253
Score = 32.7 bits (74), Expect = 0.22
Identities = 43/216 (19%), Positives = 84/216 (38%), Gaps = 34/216 (15%)
Query: 55 KRIEDGYKLCNDLIALIQERADIEKAYAKSLKGWNKKW---------------------- 92
K + G ++ I ++ER +IE +YAK L+ +KK+
Sbjct: 12 KHTQWGIEVLEKYIKFVKERTEIELSYAKQLRNLSKKYQPKKNSKEEEEYKYTSCRAFLM 71
Query: 93 -----------NELIEKVMRTCWQKDTYHKTVLHIKERKEMEDAFKKAQKPWCKLLTKVN 141
+E+I + + + + +ERK +KAQ+ ++
Sbjct: 72 TLNEMNDYAGQHEVISENLASQIIVELTRYVQELKQERKSHFHDGRKAQQHIETCWKQLE 131
Query: 142 KTKNDYHVACKAERSASNQERNASADSSLSMDQLKKMQDRVQKAKEEVQKAKEKYELALQ 201
+K + CK A AD +++ ++K + + Q + + +K +Y LQ
Sbjct: 132 SSKRRFERDCKEADRAQQYFEKMDADINVTKADVEKARQQAQIRHQMAEDSKAEYSSYLQ 191
Query: 202 ELNS-YNPKYMEDMSVVFDKCQEMETTRLQFFKDSL 236
+ N + Y + +F K QEME R+ +S+
Sbjct: 192 KFNKEQHEHYYTHIPNIFQKIQEMEERRIGRVGESM 227
>gnl|CDD|153357 cd07673, F-BAR_FCHO2, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of FCH domain Only 2
protein. F-BAR domains are dimerization modules that
bind and bend membranes and are found in proteins
involved in membrane dynamics and actin reorganization.
The specific function of FCH domain Only 2 (FCHO2) is
still unknown. It contains an N-terminal F-BAR domain
and a C-terminal domain of unknown function named SAFF
which is also present in FCHO1 and endophilin
interacting protein 1. F-BAR domains form banana-shaped
dimers with a positively-charged concave surface that
binds to negatively-charged lipid membranes. They can
induce membrane deformation in the form of long tubules.
Length = 269
Score = 32.7 bits (74), Expect = 0.26
Identities = 42/186 (22%), Positives = 84/186 (45%), Gaps = 13/186 (6%)
Query: 66 DLIALIQERADIEKAYAKSLKGWNKKWNELIE-KVMRTCW---QKDTYHKTVLHIKERKE 121
+L I+ERA IE+AY++S+ K + + W + T H++ ++
Sbjct: 30 ELSDFIRERATIEEAYSRSMTKLAKSASNYSQLGTFAPVWDVFKTSTEKLANCHLELVRK 89
Query: 122 MEDAFKKAQKPWCKLLTKVNKTKNDYHVACKAERS------ASNQERNASADSSLSMDQL 175
+++ K+ QK + + KTK + +A ++ A + + L ++L
Sbjct: 90 LQELIKEVQKYGEEQVKSHKKTKEEVAGTLEAVQNIQSITQALQKSKENYNAKCLEQERL 149
Query: 176 KK---MQDRVQKAKEEVQKAKEKYELALQELNSYNPKYMEDMSVVFDKCQEMETTRLQFF 232
KK Q ++KA + +KA E Y+L +++ + + M+ K Q++E T L
Sbjct: 150 KKEGATQREIEKAAVKSKKATESYKLYVEKYALAKADFEQKMTETAQKFQDIEETHLIRI 209
Query: 233 KDSLFS 238
K+ + S
Sbjct: 210 KEIIGS 215
>gnl|CDD|185272 PRK15374, PRK15374, pathogenicity island 1 effector protein SipB;
Provisional.
Length = 593
Score = 33.0 bits (75), Expect = 0.27
Identities = 22/98 (22%), Positives = 39/98 (39%), Gaps = 1/98 (1%)
Query: 102 TCWQKDTYHKTVLHIKERKEMEDAFKKAQKPWCKLLTKVNKTKNDYHVACKAERSASNQE 161
WQ + + I+ KE + A +AQ+ + KT V AE+ Q
Sbjct: 109 AVWQAMIESQKEMGIQVSKEFQTALGEAQEATDLYEASIKKTDTAKSVYDAAEKKL-TQA 167
Query: 162 RNASADSSLSMDQLKKMQDRVQKAKEEVQKAKEKYELA 199
+N + + + V++A +E +AKE + A
Sbjct: 168 QNKLQSLDPADPGYAQAEAAVEQAGKEATEAKEALDKA 205
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 32.5 bits (75), Expect = 0.33
Identities = 22/114 (19%), Positives = 39/114 (34%), Gaps = 16/114 (14%)
Query: 185 AKEEVQKAKEKYELALQELNSYNPKYME-DMSVVFDKCQEMET-TRLQFFKDSL---FSI 239
+ + + E Y+ EL Y+PK E VV +K L+ K +L
Sbjct: 248 SPIDGRDPIEDYQTIRNELEKYSPKLAEKPRIVVLNKIDLPLDEEELEELKKALAEALGW 307
Query: 240 HKCLNIS------QDPTVLHIKE-RKEMEDAFKKAQKPWCKTVLHIKERKEMED 286
IS D + + E +E + + A+ L ++ +D
Sbjct: 308 EVFYLISALTREGLDELLRALAELLEETKAEAEAAEAEE----LPVEVEVLYDD 357
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 32.8 bits (75), Expect = 0.35
Identities = 18/110 (16%), Positives = 49/110 (44%), Gaps = 3/110 (2%)
Query: 117 KERKEMEDAFKKAQKPWCKLLTKVNKTKND-YHVACKAERSASNQERNASADSSL--SMD 173
E +E+ + ++ Q+ +L ++ + + + + + E + E L ++
Sbjct: 274 SELEELREELEELQEELLELKEEIEELEGEISLLRERLEELENELEELEERLEELKEKIE 333
Query: 174 QLKKMQDRVQKAKEEVQKAKEKYELALQELNSYNPKYMEDMSVVFDKCQE 223
LK+ + + EE+++ + E A +EL +E++ +F+ +E
Sbjct: 334 ALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALRE 383
>gnl|CDD|216648 pfam01690, PLRV_ORF5, Potato leaf roll virus readthrough protein.
This family consists mainly of the potato leaf roll
virus readthrough protein. This is generated via a
readthrough of open reading frame 3 a coat protein
allowing transcription of open reading frame 5 to give
an extended coat protein with a large c-terminal
addition or read through domain. The readthrough protein
is thought to play a role in the circulative aphid
transmission of potato leaf roll virus. Also in the
family is open reading frame 6 from beet western yellows
virus and potato leaf roll virus both luteovirus and an
unknown protein from cucurbit aphid-borne yellows virus
a closterovirus.
Length = 460
Score = 31.6 bits (72), Expect = 0.73
Identities = 18/47 (38%), Positives = 20/47 (42%), Gaps = 12/47 (25%)
Query: 16 LSCEGAQAVLGGMSHHSDENM-----LIASSDS---FWEPGNYKRTT 54
+SCEG QAV S D N LIA + W GNY T
Sbjct: 104 ISCEGYQAV----SSTGDPNDGKWDGLIAYDNDSSDGWNVGNYNGCT 146
>gnl|CDD|153334 cd07650, F-BAR_Syp1p_like, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of yeast Syp1 protein.
F-BAR domains are dimerization modules that bind and
bend membranes and are found in proteins involved in
membrane dynamics and actin reorganization. Syp1p is
associated with septins, a family of GTP-binding
proteins that serve as elements of septin filaments,
which are required for cell morphogenesis and division.
Syp1p regulates cell-cycle dependent septin cytoskeletal
dynamics in yeast. It contains an N-terminal F-BAR
domain and a C-terminal domain of unknown function named
SAFF which is also present in FCH domain Only (FCHO)
proteins and endophilin interacting protein 1. F-BAR
domains form banana-shaped dimers with a
positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules.
Length = 228
Score = 30.8 bits (70), Expect = 0.84
Identities = 40/185 (21%), Positives = 72/185 (38%), Gaps = 31/185 (16%)
Query: 62 KLCNDLIAL-IQERADIEKAYAKSLKGWNKKWNELIEK----VMRTCWQKDTYHKTVLHI 116
KL N +A +QER +E+ Y + L+ ++ NE + K V + W T+
Sbjct: 18 KLVNTELADWLQERRRLERQYVQGLRKLARR-NEPLNKSLLGVFQNPWL------TIES- 69
Query: 117 KERKEMEDAFKKAQKPWCKLLTKVNKTKNDYHVACKAERSASNQERNAS-----ADSSLS 171
E E + ++ T V + D+ + + + + + ++ +S
Sbjct: 70 ----ETEFIAASHGELAQRIETDVEEPLRDFATSTEFMNTLDDDQNLSNLAKELDESQKK 125
Query: 172 MDQLKKMQDRVQKAKEEVQKAKEKYELALQELNSYNPKYMEDMSVVFDKCQEMETTRLQF 231
D+LKK + V A E A Q+ +S P +F+ Q ++ RL
Sbjct: 126 WDKLKKKHSKASSKA--VSAAVSDLEEARQQWDSQAPF-------LFELLQAIDEERLNH 176
Query: 232 FKDSL 236
KD L
Sbjct: 177 LKDVL 181
>gnl|CDD|215143 PLN02255, PLN02255, H(+) -translocating inorganic pyrophosphatase.
Length = 765
Score = 31.3 bits (71), Expect = 0.89
Identities = 20/60 (33%), Positives = 25/60 (41%), Gaps = 8/60 (13%)
Query: 278 IKERKEMEDAFKKAQKPWCIMQHLKLICILKCCYSRLPQIYEEFYHTINNADHEKDLKWW 337
IK KE+E A KK I L + I + LP F TI N +K +K W
Sbjct: 350 IKAVKEIEPALKKQ---LIISTVLMTVGIAVVSWLALP---SSF--TIFNFGTQKVVKNW 401
>gnl|CDD|153358 cd07674, F-BAR_FCHO1, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of FCH domain Only 1
protein. F-BAR domains are dimerization modules that
bind and bend membranes and are found in proteins
involved in membrane dynamics and actin reorganization.
FCH domain Only 1 (FCHO1) may be involved in
clathrin-coated vesicle formation. It contains an
N-terminal F-BAR domain and a C-terminal domain of
unknown function named SAFF which is also present in
FCHO2 and endophilin interacting protein 1. F-BAR
domains form banana-shaped dimers with a
positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules.
Length = 261
Score = 30.7 bits (69), Expect = 0.91
Identities = 41/202 (20%), Positives = 75/202 (37%), Gaps = 55/202 (27%)
Query: 66 DLIALIQERADIEKAYAKSLKGWNK----------------------------------K 91
+L ++ERA IE+ Y+KS+ +K K
Sbjct: 23 ELADFVRERAAIEETYSKSMSKLSKMASNGSPLGTFAPMWEVFRVSSDKLALCHLELMRK 82
Query: 92 WNELIEKVMRTCWQKDTYHKTVLHIKERKEMEDAFKKAQKPWCKLLTKVNKTKNDYHVAC 151
N+LI+ + R ++ HK K ++E + Q + + K++ +YH C
Sbjct: 83 LNDLIKDINRYGDEQVKIHK-----KTKEEAIGTLEAVQSLQVQS-QHLQKSRENYHSKC 136
Query: 152 KAERSASNQERNASADSSLSMDQLKKMQDRVQKAKEEVQKAKEKYELALQELNSYNPKYM 211
QER Q ++KA+ + +KA E ++++ N +
Sbjct: 137 ------VEQERLRREGVP---------QKELEKAELKTKKAAESLRGSVEKYNRARGDFE 181
Query: 212 EDMSVVFDKCQEMETTRLQFFK 233
+ M K Q++E T L+ K
Sbjct: 182 QKMLESAQKFQDIEETHLRHMK 203
>gnl|CDD|216872 pfam02096, 60KD_IMP, 60Kd inner membrane protein.
Length = 193
Score = 30.6 bits (70), Expect = 0.94
Identities = 8/47 (17%), Positives = 25/47 (53%), Gaps = 3/47 (6%)
Query: 165 SADSSLSMDQLKKMQDRVQKAKEEVQKAKEKYELALQEL---NSYNP 208
+ SM +++++Q +++ +E+ + +K + + +L + NP
Sbjct: 22 TLKQYKSMAKMQELQPEIKEIQEKYKDDPQKLQQEMMKLYKEHGVNP 68
>gnl|CDD|179150 PRK00876, nadE, NAD synthetase; Reviewed.
Length = 326
Score = 31.1 bits (71), Expect = 0.97
Identities = 15/33 (45%), Positives = 18/33 (54%), Gaps = 3/33 (9%)
Query: 311 YSRLPQIYEEFYHTINNADHEKDLKWWSNNHGV 343
YS LPQ EEFY + DL ++ NHGV
Sbjct: 250 YS-LPQTQEEFYFAL--PYDRMDLCLYALNHGV 279
>gnl|CDD|153356 cd07672, F-BAR_PSTPIP2, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Proline-Serine-Threonine
Phosphatase-Interacting Protein 2. F-BAR domains are
dimerization modules that bind and bend membranes and
are found in proteins involved in membrane dynamics and
actin reorganization. Proline-Serine-Threonine
Phosphatase-Interacting Protein 2 (PSTPIP2), also known
as Macrophage Actin-associated tYrosine Phosphorylated
protein (MAYP), is mostly expressed in hematopoietic
cells but is also expressed in the brain. It is involved
in regulating cell adhesion and motility. Mutations in
the gene encoding murine PSTPIP2 can cause
autoinflammatory disorders such as chronic multifocal
osteomyelitis and macrophage autoinflammatory disease.
PSTPIP2 contains an N-terminal F-BAR domain and lacks
the PEST motifs and SH3 domain that are found in
PSTPIP1. F-BAR domains form banana-shaped dimers with a
positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules.
Length = 240
Score = 30.7 bits (69), Expect = 0.98
Identities = 46/218 (21%), Positives = 97/218 (44%), Gaps = 32/218 (14%)
Query: 48 GNYKRTTKRIEDGYKLCNDLIALIQERADIEKAYAKSLKGWNKK---WNELIEKVMRT-- 102
G Y + + DG K C + ++ERA IE+ Y K L +KK I + R+
Sbjct: 5 GGYDCIIQHLNDGRKNCKEFEDFLKERASIEEKYGKELLNLSKKKPCGQTEINTLKRSLD 64
Query: 103 CWQKDTYHKTVLHIK-------ERKEMEDAFKKAQKPWCKLL---------------TKV 140
+++ + HI+ E K+MED F++ QK K + K
Sbjct: 65 VFKQQIDNVGQSHIQLAQTLRDEAKKMED-FRERQKLARKKIELIMDAIHKQRAMQFKKT 123
Query: 141 NKTKNDYHVACKAERSASNQERNASADSSLS-MDQLKKMQDRVQKAKEEVQKAKEKYELA 199
++K +Y C+ + A E+ + +++L + Q +K+ ++ ++K+ + A Y
Sbjct: 124 MESKKNYEQKCRDKDEA---EQAVNRNANLVNVKQQEKLFAKLAQSKQNAEDADRLYMQN 180
Query: 200 LQELNSYNPKYMEDMSVVFDKCQEMETTRLQFFKDSLF 237
+ L+ + ++ + ++ E R+ FF+++++
Sbjct: 181 ISVLDKIREDWQKEHVKACEFFEKQECERINFFRNAVW 218
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 30.8 bits (70), Expect = 1.3
Identities = 21/90 (23%), Positives = 47/90 (52%)
Query: 116 IKERKEMEDAFKKAQKPWCKLLTKVNKTKNDYHVACKAERSASNQERNASADSSLSMDQL 175
IKE +E E+ ++ +K +L ++ + + + + +A+ ER + L+ ++L
Sbjct: 330 IKELEEKEERLEELKKKLKELEKRLEELEERHELYEEAKAKKEELERLKKRLTGLTPEKL 389
Query: 176 KKMQDRVQKAKEEVQKAKEKYELALQELNS 205
+K + ++KAKEE+++ K + EL
Sbjct: 390 EKELEELEKAKEEIEEEISKITARIGELKK 419
>gnl|CDD|217803 pfam03938, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 157
Score = 29.5 bits (67), Expect = 1.3
Identities = 20/107 (18%), Positives = 46/107 (42%), Gaps = 18/107 (16%)
Query: 117 KERKEMEDAFKKAQKPWCKLLTKVNKTKNDYHVACKAERSASNQERNASADSSLSMDQLK 176
K + +K K KL ++ K + + + E ++ ++LS + K
Sbjct: 31 PAGKAAQKQLEKEFK---KLQAELQKKEKEL----QKEEQKLQKQA-----ATLSEEARK 78
Query: 177 KMQDRVQKAKEEVQKAKEKYELALQELNSYNPKYMEDMSVVFDKCQE 223
Q +Q+ ++E+Q+ ++ + LQ+ K E + ++DK +
Sbjct: 79 AKQQELQQKQQELQQKQQAAQQELQQ------KQQELLQPIYDKIDK 119
>gnl|CDD|240360 PTZ00325, PTZ00325, malate dehydrogenase; Provisional.
Length = 321
Score = 30.4 bits (69), Expect = 1.4
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 169 SLSMDQLKKMQDRVQKAKEEVQKAKEK 195
SL +Q++++ RVQ +EV KAKE
Sbjct: 199 SLPEEQVEQITHRVQVGGDEVVKAKEG 225
>gnl|CDD|218630 pfam05546, She9_MDM33, She9 / Mdm33 family. Members of this family
are mitochondrial inner membrane proteins with a role in
inner mitochondrial membrane organisation and
biogenesis.
Length = 208
Score = 30.0 bits (68), Expect = 1.5
Identities = 13/36 (36%), Positives = 25/36 (69%), Gaps = 4/36 (11%)
Query: 171 SMDQLKK----MQDRVQKAKEEVQKAKEKYELALQE 202
S+++LKK ++ +++ AKEEV++AK+ Y A+
Sbjct: 33 SIEKLKKSIEELETQLRAAKEEVREAKKAYSEAIAR 68
>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175).
Length = 820
Score = 30.6 bits (70), Expect = 1.5
Identities = 14/69 (20%), Positives = 32/69 (46%), Gaps = 11/69 (15%)
Query: 153 AERSASNQERNASADS-----SLSMDQLKKMQDRVQKAKEEVQKAKEKYELALQELNSYN 207
AE++ N ++ L+ L++M DR+++ E + + + L++L
Sbjct: 513 AEQAQRNPQQGDQPPDQGNSMELTQQDLQRMMDRIEELME--SGRRAEAQQLLEQLQ--- 567
Query: 208 PKYMEDMSV 216
+ ME++ V
Sbjct: 568 -QMMENLQV 575
>gnl|CDD|224455 COG1538, TolC, Outer membrane protein [Cell envelope biogenesis,
outer membrane / Intracellular trafficking and
secretion].
Length = 457
Score = 30.1 bits (68), Expect = 1.8
Identities = 9/44 (20%), Positives = 22/44 (50%)
Query: 159 NQERNASADSSLSMDQLKKMQDRVQKAKEEVQKAKEKYELALQE 202
A + + ++ L+ +++Q ++ V+ A+E ELA +
Sbjct: 356 QTVLTARQEVADALAALEAALEQLQALRQAVEAAQEALELARER 399
>gnl|CDD|129587 TIGR00496, frr, ribosome recycling factor. This model finds only
eubacterial proteins. Mitochondrial and/or chloroplast
forms might be expected but are not currently known.
This protein was previously called ribosome releasing
factor. By releasing ribosomes from mRNA at the end of
protein biosynthesis, it prevents inappropriate
translation from 3-prime regions of the mRNA and frees
the ribosome for new rounds of translation.
EGAD|53116|YHR038W is part of the frr superfamily
[Protein synthesis, Translation factors].
Length = 176
Score = 29.3 bits (66), Expect = 2.0
Identities = 13/48 (27%), Positives = 26/48 (54%), Gaps = 7/48 (14%)
Query: 155 RSASNQERNASADSSLSMDQLKKMQDRVQKAK-------EEVQKAKEK 195
R A+++ + D +S D+ +++Q+ +QK +E+ K KEK
Sbjct: 124 RDANDKVKKLEKDKEISEDEERRLQEEIQKLTDEYIKKIDEILKDKEK 171
>gnl|CDD|173089 PRK14626, PRK14626, hypothetical protein; Provisional.
Length = 110
Score = 28.7 bits (64), Expect = 2.2
Identities = 9/22 (40%), Positives = 18/22 (81%)
Query: 172 MDQLKKMQDRVQKAKEEVQKAK 193
M Q++ +++ V+KAKEE++K +
Sbjct: 11 MKQMQSIKENVEKAKEELKKEE 32
>gnl|CDD|217163 pfam02646, RmuC, RmuC family. This family contains several
bacterial RmuC DNA recombination proteins. The function
of the RMUC protein is unknown but it is suspected that
it is either a structural protein that protects DNA
against nuclease action, or is itself involved in DNA
cleavage at the regions of DNA secondary structures.
Length = 301
Score = 29.6 bits (67), Expect = 2.3
Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 159 NQERNASADSSLS---MDQLKKMQDRVQKAKEEVQKAKEKYELALQELNS 205
E+NA + L+ D+ K DR++K + +++A + Y+ AL L +
Sbjct: 226 RIEKNAKEIAELAGELYDEFGKFADRLEKLGKHLEQAVKSYDDALNSLTT 275
>gnl|CDD|226055 COG3524, KpsE, Capsule polysaccharide export protein [Cell envelope
biogenesis, outer membrane].
Length = 372
Score = 29.8 bits (67), Expect = 2.4
Identities = 14/36 (38%), Positives = 22/36 (61%)
Query: 175 LKKMQDRVQKAKEEVQKAKEKYELALQELNSYNPKY 210
+ +D V+ A+EEVQKA+E+ + A +L Y K
Sbjct: 174 ERARRDTVRFAEEEVQKAEERVKKASNDLTDYRIKN 209
>gnl|CDD|233229 TIGR00999, 8a0102, Membrane Fusion Protein cluster 2 (function with
RND porters). [Transport and binding proteins, Other].
Length = 265
Score = 29.3 bits (66), Expect = 2.6
Identities = 22/90 (24%), Positives = 35/90 (38%), Gaps = 15/90 (16%)
Query: 118 ERKEMEDAFKKAQKPWCKLLTKVNKTKNDYHVACKAERSASNQERNASADSSL--SMDQL 175
E +M K AQK +V + Y ER E+ + L
Sbjct: 17 ELAKMAAELKVAQK-------RVELARKTY------EREKKLFEQGVIPRQEFESAEYAL 63
Query: 176 KKMQDRVQKAKEEVQKAKEKYELALQELNS 205
++ Q VQ AK E++ A+E + + E+ S
Sbjct: 64 EEAQAEVQAAKSELRSAREAKDGSYVEVRS 93
>gnl|CDD|215656 pfam00012, HSP70, Hsp70 protein. Hsp70 chaperones help to fold
many proteins. Hsp70 assisted folding involves repeated
cycles of substrate binding and release. Hsp70 activity
is ATP dependent. Hsp70 proteins are made up of two
regions: the amino terminus is the ATPase domain and the
carboxyl terminus is the substrate binding region.
Length = 598
Score = 29.5 bits (67), Expect = 2.8
Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 148 HVACKAERSASNQERNASADSSLSMDQLKKMQDRVQKAKEEVQKAKEKYELALQELNSY 206
V+ K + + Q+ +A S LS D++++M ++ E +K KE+ E A E Y
Sbjct: 479 TVSAKDKGTGKEQKITITASSGLSDDEIERMVKDAEEYAAEDKKRKERIE-AKNEAEEY 536
>gnl|CDD|220366 pfam09728, Taxilin, Myosin-like coiled-coil protein. Taxilin
contains an extraordinarily long coiled-coil domain in
its C-terminal half and is ubiquitously expressed. It is
a novel binding partner of several syntaxin family
members and is possibly involved in Ca2+-dependent
exocytosis in neuroendocrine cells. Gamma-taxilin,
described as leucine zipper protein Factor Inhibiting
ATF4-mediated Transcription (FIAT), localises to the
nucleus in osteoblasts and dimerises with ATF4 to form
inactive dimers, thus inhibiting ATF4-mediated
transcription.
Length = 309
Score = 28.9 bits (65), Expect = 3.7
Identities = 28/144 (19%), Positives = 58/144 (40%), Gaps = 3/144 (2%)
Query: 126 FKKAQKPWCKLLTKVNKTKNDYHVACKAERSASNQERNASADSSLS---MDQLKKMQDRV 182
KKA + + L+K++ + K + + D +QL+K +D++
Sbjct: 3 VKKAARLLNQSLSKLDTPEEKLETLIKRLAELLKEMKRLEKDLKKLQKRGEQLQKEKDKL 62
Query: 183 QKAKEEVQKAKEKYELALQELNSYNPKYMEDMSVVFDKCQEMETTRLQFFKDSLFSIHKC 242
Q + A+ K E +EL +N E+ D+ +E + F+ +L I
Sbjct: 63 QSEHSKAILARSKLESLCRELQKHNKTLKEENKARSDEEEEKRKELTEKFQSTLKDIQDQ 122
Query: 243 LNISQDPTVLHIKERKEMEDAFKK 266
+ +P +E +E+ + K+
Sbjct: 123 MEEHSNPNHKLCEENEELREKLKE 146
>gnl|CDD|224241 COG1322, COG1322, Predicted nuclease of restriction
endonuclease-like fold, RmuC family [General function
prediction only].
Length = 448
Score = 29.3 bits (66), Expect = 3.7
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 159 NQERNASADSSLS---MDQLKKMQDRVQKAKEEVQKAKEKYELALQELNS 205
QE+NA + D+ K DR++K + +Q+A + Y+ AL L S
Sbjct: 349 RQEKNAKEIAEEVGKLYDEFGKFADRLEKLGKHLQQAVKSYDQALNSLTS 398
>gnl|CDD|130833 TIGR01772, MDH_euk_gproteo, malate dehydrogenase, NAD-dependent.
This model represents the NAD-dependent malate
dehydrogenase found in eukaryotes and certain gamma
proteobacteria. The enzyme is involved in the citric
acid cycle as well as the glyoxalate cycle. Several
isoforms exidt in eukaryotes. In S. cereviseae, for
example, there are cytoplasmic, mitochondrial and
peroxisomal forms. Although malate dehydrogenases have
in some cases been mistaken for lactate dehydrogenases
due to the similarity of these two substrates and the
apparent ease with which evolution can toggle these
activities, critical residues have been identified which
can discriminate between the two activities. At the time
of the creation of this model no hits above the trusted
cutoff contained critical residues typical of lactate
dehydrogenases [Energy metabolism, TCA cycle].
Length = 312
Score = 28.9 bits (65), Expect = 4.0
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 168 SSLSMDQLKKMQDRVQKAKEEVQKAK 193
+ DQL+ + R+Q A EV KAK
Sbjct: 191 VLFTEDQLEALIHRIQNAGTEVVKAK 216
>gnl|CDD|153341 cd07657, F-BAR_Fes_Fer, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Fes (feline sarcoma) and
Fer (Fes related) tyrosine kinases. F-BAR domains are
dimerization modules that bind and bend membranes and
are found in proteins involved in membrane dynamics and
actin reorganization. Fes (feline sarcoma), also called
Fps (Fujinami poultry sarcoma), and Fer (Fes related)
are cytoplasmic (or nonreceptor) tyrosine kinases that
play roles in haematopoiesis, inflammation and immunity,
growth factor signaling, cytoskeletal regulation, cell
migration and adhesion, and the regulation of cell-cell
interactions. Although Fes and Fer show redundancy in
their biological functions, they show differences in
their expression patterns. Fer is ubiquitously expressed
while Fes is expressed predominantly in myeloid and
endothelial cells. Fes and Fer contain an N-terminal
F-BAR domain, an SH2 domain, and a C-terminal catalytic
kinase domain. F-BAR domains form banana-shaped dimers
with a positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules. The
F-BAR domain of Fes is critical in its role in
microtubule nucleation and bundling.
Length = 237
Score = 28.9 bits (65), Expect = 4.1
Identities = 25/101 (24%), Positives = 48/101 (47%), Gaps = 4/101 (3%)
Query: 108 TYHKTVLHIKERKEMEDAF----KKAQKPWCKLLTKVNKTKNDYHVACKAERSASNQERN 163
T K L IK++++ + A+ ++ + + KL +V K K++Y + ++A ++
Sbjct: 92 TLDKLTLLIKDKRKAKKAYQEERQQIDEQYKKLTDEVEKLKSEYQKLLEDYKAAKSKFEE 151
Query: 164 ASADSSLSMDQLKKMQDRVQKAKEEVQKAKEKYELALQELN 204
A +L K +D+ QKA ++ Y LAL E
Sbjct: 152 AVVKGGRGGRKLDKARDKYQKACRKLHLCHNDYVLALLEAQ 192
>gnl|CDD|198395 cd10448, GIY-YIG_unchar_3, GIY-YIG domain of uncharacterized
hypothetical protein found in bacteria. The family
includes a group of uncharacterized bacterial proteins
with a GIY-YIG domain that shows statistically
significant similarity to the N-terminal catalytic
domains of GIY-YIG family of intron-encoded homing
endonuclease I-TevI and catalytic GIY-YIG domain of
nucleotide excision repair endonuclease UvrC.
Length = 87
Score = 27.1 bits (61), Expect = 4.6
Identities = 14/27 (51%), Positives = 17/27 (62%), Gaps = 3/27 (11%)
Query: 76 DIEKAYA--KSLKGWNKKW-NELIEKV 99
DIE+A A K LK W + W LIEK+
Sbjct: 54 DIEEAIAREKQLKKWRRAWKINLIEKM 80
>gnl|CDD|216689 pfam01765, RRF, Ribosome recycling factor. The ribosome recycling
factor (RRF / ribosome release factor) dissociates the
ribosome from the mRNA after termination of translation,
and is essential bacterial growth. Thus ribosomes are
"recycled" and ready for another round of protein
synthesis.
Length = 165
Score = 27.8 bits (63), Expect = 5.1
Identities = 14/40 (35%), Positives = 25/40 (62%), Gaps = 7/40 (17%)
Query: 171 SMDQLKKMQ-------DRVQKAKEEVQKAKEKYELALQEL 203
+ D+LKK++ D V++A++E+QK +KY + EL
Sbjct: 117 ANDKLKKLEKDKEISEDEVKRAEKEIQKLTDKYIKKIDEL 156
Score = 27.5 bits (62), Expect = 7.8
Identities = 17/69 (24%), Positives = 33/69 (47%), Gaps = 8/69 (11%)
Query: 135 KLLTKVNKTKNDYHVACKAERSASNQE-RNASADSSLSMDQLKKMQDRVQKAK------- 186
+L+ + K + VA + R +N + + D +S D++K+ + +QK
Sbjct: 94 ELVKQAKKLAEEAKVAIRNIRRDANDKLKKLEKDKEISEDEVKRAEKEIQKLTDKYIKKI 153
Query: 187 EEVQKAKEK 195
+E+ K KEK
Sbjct: 154 DELLKKKEK 162
>gnl|CDD|223311 COG0233, Frr, Ribosome recycling factor [Translation, ribosomal
structure and biogenesis].
Length = 187
Score = 28.3 bits (64), Expect = 5.1
Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 9/70 (12%)
Query: 135 KLLTKVNKTK-NDYHVACKAERSASNQE-RNASADSSLSMDQLKKMQDRVQKAK------ 186
K L KV K + VA + R +N + + D +S D++KK ++ +QK
Sbjct: 113 KELVKVAKKYAEEAKVAVRNIRRDANDKIKKLEKDKEISEDEVKKAEEEIQKLTDEYIKK 172
Query: 187 -EEVQKAKEK 195
+E+ K KEK
Sbjct: 173 IDELLKDKEK 182
>gnl|CDD|182860 PRK10949, PRK10949, protease 4; Provisional.
Length = 618
Score = 28.9 bits (65), Expect = 5.6
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 61 YKLCNDLIALIQERADIEKAYAKSLKGWNKKWN 93
Y L N L+ + A+IEKA K+ GW+K
Sbjct: 275 YALDNKLVDALASSAEIEKALTKAF-GWSKTDK 306
>gnl|CDD|151614 pfam11172, DUF2959, Protein of unknown function (DUF2959). This
family of proteins with unknown function appears to be
restricted to Gammaproteobacteria.
Length = 201
Score = 28.0 bits (63), Expect = 5.9
Identities = 9/28 (32%), Positives = 21/28 (75%)
Query: 178 MQDRVQKAKEEVQKAKEKYELALQELNS 205
+ DRV+ A++ + A+E+++ AL++ +S
Sbjct: 26 LVDRVEDARDSQEDAQEQFKSALEQFSS 53
>gnl|CDD|133422 cd01337, MDH_glyoxysomal_mitochondrial, Glyoxysomal and
mitochondrial malate dehydrogenases. MDH is one of the
key enzymes in the citric acid cycle, facilitating both
the conversion of malate to oxaloacetate and
replenishing levels of oxalacetate by reductive
carboxylation of pyruvate. Members of this subfamily are
localized to the glycosome and mitochondria. MDHs are
part of the NAD(P)-binding Rossmann fold superfamily,
which includes a wide variety of protein families
including the NAD(P)-binding domains of alcohol
dehydrogenases, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 310
Score = 28.2 bits (64), Expect = 6.2
Identities = 7/27 (25%), Positives = 15/27 (55%)
Query: 168 SSLSMDQLKKMQDRVQKAKEEVQKAKE 194
+ ++++ + R+Q +EV KAK
Sbjct: 192 FTFDQEEIEALTHRIQFGGDEVVKAKA 218
>gnl|CDD|153272 cd07588, BAR_Amphiphysin, The Bin/Amphiphysin/Rvs (BAR) domain of
Amphiphysins. BAR domains are dimerization, lipid
binding and curvature sensing modules found in many
different proteins with diverse functions. Amphiphysins
function primarily in endocytosis and other membrane
remodeling events. They contain an N-terminal BAR domain
with an additional N-terminal amphipathic helix (an
N-BAR), a variable central domain, and a C-terminal SH3
domain. This subfamily is composed of different isoforms
of amphiphysin and Bridging integrator 2 (Bin2).
Amphiphysin I proteins, enriched in the brain and
nervous system, contain domains that bind clathrin,
Adaptor Protein complex 2 (AP2), dynamin and
synaptojanin. They function in synaptic vesicle
endocytosis. Some amphiphysin II isoforms, also called
Bridging integrator 1 (Bin1), are localized in many
different tissues and may function in intracellular
vesicle trafficking. In skeletal muscle, Bin1 plays a
role in the organization and maintenance of the T-tubule
network. Bin2 is mainly expressed in hematopoietic cells
and is upregulated during granulocyte differentiation.
The N-BAR domains of amphiphysins form a curved dimer
with a positively-charged concave face that can drive
membrane bending and curvature.
Length = 211
Score = 28.1 bits (63), Expect = 6.4
Identities = 21/64 (32%), Positives = 37/64 (57%), Gaps = 14/64 (21%)
Query: 176 KKMQDRVQKAKEEVQKAKEKYELALQELNSYNPKYMEDMSVVFDKCQEMETTRLQFFKDS 235
K ++ KA+EE+Q+AK+ YE ELN+ + E++ ++D +R+ F+ D+
Sbjct: 135 KVDDQKLTKAEEELQQAKKVYE----ELNT---ELHEELPALYD-------SRIAFYVDT 180
Query: 236 LFSI 239
L SI
Sbjct: 181 LQSI 184
>gnl|CDD|217843 pfam04012, PspA_IM30, PspA/IM30 family. This family includes PspA
a protein that suppresses sigma54-dependent
transcription. The PspA protein, a negative regulator of
the Escherichia coli phage shock psp operon, is produced
when virulence factors are exported through secretins in
many Gram-negative pathogenic bacteria and its homologue
in plants, VIPP1, plays a critical role in thylakoid
biogenesis, essential for photosynthesis. Activation of
transcription by the enhancer-dependent bacterial
sigma(54) containing RNA polymerase occurs through ATP
hydrolysis-driven protein conformational changes enabled
by activator proteins that belong to the large AAA(+)
mechanochemical protein family. It has been shown that
PspA directly and specifically acts upon and binds to
the AAA(+) domain of the PspF transcription activator.
Length = 220
Score = 28.1 bits (63), Expect = 6.5
Identities = 21/128 (16%), Positives = 50/128 (39%), Gaps = 8/128 (6%)
Query: 72 QERADIEKAYAKSLKGWNKKWNELIEKVMRTCWQKDTYHKTVL-HIKERKEMEDAFKKAQ 130
+++ +K K+ K EL + + + T K + + A ++ +
Sbjct: 62 EQKEQAKKLENKARAALTKGNEELAREALA---EIATLEKQAEALETQLTQQRSAVEQLR 118
Query: 131 KPWCKLLTKVNKTKNDYHVACKAERSASNQE----RNASADSSLSMDQLKKMQDRVQKAK 186
K L TK+ + K ++A QE SA + + D +++++++++ +
Sbjct: 119 KQLAALETKIQQLKAKKTALKARLKAAKAQEAVNTSLGSASTESATDSFERIEEKIEERE 178
Query: 187 EEVQKAKE 194
A E
Sbjct: 179 ARADAAAE 186
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 28.5 bits (64), Expect = 6.7
Identities = 10/51 (19%), Positives = 25/51 (49%), Gaps = 7/51 (13%)
Query: 174 QLKKMQDRVQKAKEEVQKA-------KEKYELALQELNSYNPKYMEDMSVV 217
QL++++ ++++ + +++K K K E +EL+ ED +
Sbjct: 897 QLRELERKIEELEAQIEKKRKRLSELKAKLEALEEELSEIEDPKGEDEEIP 947
>gnl|CDD|233288 TIGR01139, cysK, cysteine synthase A. This model distinguishes
cysteine synthase A (CysK) from cysteine synthase B
(CysM). CysM differs in having a broader specificity
that also allows the use of thiosulfate to produce
cysteine thiosulfonate [Amino acid biosynthesis, Serine
family].
Length = 298
Score = 28.1 bits (63), Expect = 6.9
Identities = 9/35 (25%), Positives = 15/35 (42%)
Query: 176 KKMQDRVQKAKEEVQKAKEKYELALQELNSYNPKY 210
+ M+ + KA+E Y + Q N NP+
Sbjct: 113 EGMKGAIAKAEEIAASTPNSYFMLQQFENPANPEI 147
>gnl|CDD|220839 pfam10661, EssA, WXG100 protein secretion system (Wss), protein
EssA. The WXG100 protein secretion system (Wss) is
responsible for the secretion of WXG100 proteins
(pfam06013) such as ESAT-6 and CFP-10 in Mycobacterium
tuberculosis or EsxA and EsxB in Staphylococcus aureus.
In S. aureus, the Wss seems to be encoded by a locus of
eight CDS, called ess (eSAT-6 secretion system). This
locus encodes, amongst several other proteins, EssA, a
protein predicted to possess one transmembrane domain.
Due to its predicted membrane location and its absolute
requirement for WXG100 protein secretion, it has been
speculated that EssA could form a secretion apparatus in
conjunction with the polytopic membrane protein EsaA,
YukC (pfam10140) and YukAB, which is a membrane-bound
ATPase containing Ftsk/SpoIIIE domains (pfam01580)
called EssC in S. aureus and Snm1/Snm2 in Mycobacterium
tuberculosis. Proteins homologous to EssA, YukC, EsaA
and YukD seem absent from mycobacteria.
Length = 145
Score = 27.5 bits (61), Expect = 7.7
Identities = 22/85 (25%), Positives = 43/85 (50%), Gaps = 6/85 (7%)
Query: 164 ASADSSLSMDQLKKMQ-DRVQKAKEEVQKAK-EKYELALQELNSYNPKYMEDMSVVFDKC 221
++ADS L D + + DR+QK +E + K + EL + + + E+++ K
Sbjct: 3 SAADSYLEDDGKMQFKVDRLQKTDQEKNEKKLRETELDKLGIELFTTETEEEIN----KK 58
Query: 222 QEMETTRLQFFKDSLFSIHKCLNIS 246
+ E ++ ++SLFS K N++
Sbjct: 59 KNAEQKEMEDIENSLFSEDKEGNVA 83
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 28.6 bits (63), Expect = 7.9
Identities = 27/119 (22%), Positives = 51/119 (42%), Gaps = 2/119 (1%)
Query: 78 EKAYAKSLKGWNKKWNELIEKVMRTCWQKDTYHKTVLHIKERKEMEDAFKKAQ--KPWCK 135
EK A K ++ + +++ + K + +E+K+ ++A KKA+ K +
Sbjct: 1389 EKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADE 1448
Query: 136 LLTKVNKTKNDYHVACKAERSASNQERNASADSSLSMDQLKKMQDRVQKAKEEVQKAKE 194
K + K KAE + E A+ + D+ KK + +K +E +KA E
Sbjct: 1449 AKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAE 1507
>gnl|CDD|217115 pfam02575, YbaB_DNA_bd, YbaB/EbfC DNA-binding family. This is a
family of DNA-binding proteins. Members of this family
form homodimers which bind DNA via a tweezer-like
structure. The conformation of the DNA is changed when
bound to these proteins. In bacteria, these proteins may
play a role in DNA replication-recovery following DNA
damage.
Length = 92
Score = 26.3 bits (59), Expect = 8.0
Identities = 8/17 (47%), Positives = 15/17 (88%)
Query: 172 MDQLKKMQDRVQKAKEE 188
M Q ++MQ++++KA+EE
Sbjct: 1 MKQAQQMQEKMEKAQEE 17
>gnl|CDD|182183 PRK09986, PRK09986, DNA-binding transcriptional activator XapR;
Provisional.
Length = 294
Score = 27.8 bits (62), Expect = 8.3
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 243 LNISQDPTVLHIKE 256
LNISQ P +HIKE
Sbjct: 31 LNISQPPLSIHIKE 44
>gnl|CDD|234541 TIGR04320, Surf_Exclu_PgrA, SEC10/PgrA surface exclusion domain.
This model describes a conserved domain found in surface
proteins of a number of Firmutes. Many members have
LPXTG C-terminal anchoring motifs and a substantial
number have the KxYKxGKxW putative sorting signal at the
N-terminus. The tetracycline resistance plasmid pCF10 in
Enterococcus faecalis promotes conjugal plasmid transfer
in response to sex pheromones, but PgrA/Sec10 encoded by
that plasmid, a member of this family, specifically
inhibits the ability of cells to receive homologous
plasmids. The phenomenon is called surface exclusion.
Length = 356
Score = 28.2 bits (63), Expect = 8.5
Identities = 18/81 (22%), Positives = 29/81 (35%), Gaps = 10/81 (12%)
Query: 125 AFKKAQKPWCKLLTKVNKTKNDYHVACKAERSASNQERNASADSSLSMDQLKKMQDRVQK 184
A AQ T + A + E + + + +A + L Q +
Sbjct: 276 ALNTAQAALTTAQTAYAAAQAALATA-QKELANAQAQALQTAQN-----NLATAQAALAN 329
Query: 185 AKEEVQKAKEKYELALQELNS 205
A+ + KAKE AL LN+
Sbjct: 330 AEARLAKAKE----ALANLNA 346
>gnl|CDD|153332 cd07648, F-BAR_FCHO, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of FCH domain Only proteins.
F-BAR domains are dimerization modules that bind and
bend membranes and are found in proteins involved in
membrane dynamics and actin reorganization. Proteins in
this group have been named FCH domain Only (FCHO)
proteins. Vertebrates have two members, FCHO1 and FCHO2.
These proteins contain an F-BAR domain and a C-terminal
domain of unknown function named SAFF which is also
present in endophilin interacting protein 1. F-BAR
domains form banana-shaped dimers with a
positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules.
Length = 261
Score = 27.7 bits (62), Expect = 8.6
Identities = 24/97 (24%), Positives = 42/97 (43%), Gaps = 15/97 (15%)
Query: 140 VNKTKNDYHVACKAERSASNQERNASADSSLSMDQLKKMQDRVQKAKEEVQKAKEKYELA 199
+ K K YH C ER ++S +++K + +++KA++E + EKY
Sbjct: 125 LQKAKEAYHARC------LELERLRRENAS--PKEIEKAEAKLKKAQDEYKALVEKYNNI 176
Query: 200 LQELNSYNPKYMEDMSVVFDKCQEMETTRLQFFKDSL 236
+ M D F QE+E + L+ K+ L
Sbjct: 177 RADFE----TKMTDSCKRF---QEIEESHLRQMKEFL 206
>gnl|CDD|153370 cd07686, F-BAR_Fer, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Fer (Fes related)
tyrosine kinase. F-BAR domains are dimerization modules
that bind and bend membranes and are found in proteins
involved in membrane dynamics and actin reorganization.
Fer (Fes related) is a cytoplasmic (or nonreceptor)
tyrosine kinase expressed in a wide variety of tissues,
and is found to reside in both the cytoplasm and the
nucleus. It plays important roles in neuronal
polarization and neurite development, cytoskeletal
reorganization, cell migration, growth factor signaling,
and the regulation of cell-cell interactions mediated by
adherens junctions and focal adhesions. Fer kinase also
regulates cell cycle progression in malignant cells. It
contains an N-terminal F-BAR domain, an SH2 domain, and
a C-terminal catalytic kinase domain. F-BAR domains form
banana-shaped dimers with a positively-charged concave
surface that binds to negatively-charged lipid
membranes. They can induce membrane deformation in the
form of long tubules.
Length = 234
Score = 27.7 bits (61), Expect = 8.7
Identities = 26/130 (20%), Positives = 60/130 (46%), Gaps = 10/130 (7%)
Query: 110 HKTVLHIKERKEMEDAFKKAQKPWCKLLTKVNKT-----KNDYHVACKAERSASNQERNA 164
H+ + IK++++++ ++ + + KV KT K Y K SA + ++A
Sbjct: 94 HRLTMMIKDKQQVKKSYIGVHQQIEAEMYKVTKTELEKLKCSYRQLTKEVNSAKEKYKDA 153
Query: 165 SADSSLSMDQLKKMQDRVQKAKEEVQKAKEKYELALQELNSYNPKYME-DMSVVFDKCQE 223
A + +K ++R KA ++ +Y LA++ + +Y + + ++ D Q+
Sbjct: 154 VAKGK----ETEKARERYDKATMKLHMLHNQYVLAVKGAQLHQHQYYDFTLPLLLDSLQK 209
Query: 224 METTRLQFFK 233
M+ ++ K
Sbjct: 210 MQEEMIKALK 219
>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
Length = 1465
Score = 28.3 bits (63), Expect = 8.7
Identities = 36/146 (24%), Positives = 56/146 (38%), Gaps = 16/146 (10%)
Query: 57 IEDGYKLCNDLIALIQERADIEKAYAKSLKGWNKKWNELIEKVMRTCWQKDTYHKTVLHI 116
+E +LC D L E D++K KSL W K + L EK + ++D
Sbjct: 1125 LEKVQELCADRDKLNIEVEDLKKTTPKSL--WLKDLDAL-EKELDKLDKEDA-------- 1173
Query: 117 KERKEMEDAFKKAQKPWCKLLTKVNKTKNDYHVACKAERSASNQERNASADSSLSMD--- 173
K + E + A + KV++ K + AS E S +M+
Sbjct: 1174 KAEEAREKLQRAAARGESGAAKKVSRQAPKKPAPKKTTKKASESETTEETYGSSAMETEN 1233
Query: 174 --QLKKMQDRVQKAKEEVQKAKEKYE 197
++ K + R K+ AKEK E
Sbjct: 1234 VAEVVKPKGRAGAKKKAPAAAKEKEE 1259
>gnl|CDD|130673 TIGR01612, 235kDa-fam, reticulocyte binding/rhoptry protein. This
model represents a group of paralogous families in
plasmodium species alternately annotated as reticulocyte
binding protein, 235-kDa family protein and rhoptry
protein. Rhoptry protein is localized on the cell surface
and is extremely large (although apparently lacking in
repeat structure) and is important for the process of
invasion of the RBCs by the parasite. These proteins are
found in P. falciparum, P. vivax and P. yoelii.
Length = 2757
Score = 28.1 bits (62), Expect = 9.0
Identities = 32/122 (26%), Positives = 52/122 (42%), Gaps = 12/122 (9%)
Query: 124 DAFKKAQKPWCKLLTKVNKTKNDYHVACKAERSASNQER-----------NASADSSLSM 172
D ++ +K ++TK++K KN Y K + E+ N S +L
Sbjct: 1166 DDPEEIEKKIENIVTKIDKKKNIYDEIKKLLNEIAEIEKDKTSLEEVKGINLSYGKNLGK 1225
Query: 173 DQLKKMQDRVQKAKEEVQKAKEKYELALQELNSYNPKYMEDMSVVFDKCQEMETTRLQFF 232
L+K+ D +K E + KA E Y L E+ +P+ +M + D EMET +
Sbjct: 1226 LFLEKI-DEEKKKSEHMIKAMEAYIEDLDEIKEKSPEIENEMGIEMDIKAEMETFNISHD 1284
Query: 233 KD 234
D
Sbjct: 1285 DD 1286
>gnl|CDD|178263 PLN02657, PLN02657, 3,8-divinyl protochlorophyllide a 8-vinyl
reductase.
Length = 390
Score = 27.8 bits (62), Expect = 9.7
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 182 VQKAKEEVQKAKEKYELALQELNS 205
VQK E Q+AK K+E LQ L+S
Sbjct: 185 VQKPLLEFQRAKLKFEAELQALDS 208
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
0.317 0.130 0.399
Gapped
Lambda K H
0.267 0.0812 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,440,842
Number of extensions: 1606031
Number of successful extensions: 3038
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2884
Number of HSP's successfully gapped: 215
Length of query: 361
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 263
Effective length of database: 6,590,910
Effective search space: 1733409330
Effective search space used: 1733409330
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (26.7 bits)