RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18194
(157 letters)
>gnl|CDD|238661 cd01365, KISc_KIF1A_KIF1B, Kinesin motor domain, KIF1_like
proteins. KIF1A (Unc104) transports synaptic vesicles to
the nerve terminal, KIF1B has been implicated in
transport of mitochondria. Both proteins are expressed
in neurons. This catalytic (head) domain has ATPase
activity and belongs to the larger group of P-loop
NTPases. Kinesins are microtubule-dependent molecular
motors that play important roles in intracellular
transport and in cell division. In most kinesins, the
motor domain is found at the N-terminus (N-type). N-type
kinesins are (+) end-directed motors, i.e. they
transport cargo towards the (+) end of the microtubule.
In contrast to the majority of dimeric kinesins, most
KIF1A/Unc104 kinesins are monomeric motors. A
lysine-rich loop in KIF1A binds to the negatively
charged C-terminus of tubulin and compensates for the
lack of a second motor domain, allowing KIF1A to move
processively.
Length = 356
Score = 68.1 bits (167), Expect = 3e-14
Identities = 23/35 (65%), Positives = 28/35 (80%)
Query: 1 MVACLSPADNNYDETLSTLRYANRAKNIANKPHIN 35
M+A +SPAD NY+ETLSTLRYA+RAK I N +N
Sbjct: 322 MIATISPADINYEETLSTLRYADRAKKIVNVAVVN 356
>gnl|CDD|238667 cd01371, KISc_KIF3, Kinesin motor domain, kinesins II or KIF3_like
proteins. Subgroup of kinesins, which form heterotrimers
composed of 2 kinesins and one non-motor accessory
subunit. Kinesins II play important roles in ciliary
transport, and have been implicated in neuronal
transport, melanosome transport, the secretory pathway,
and mitosis. This catalytic (head) domain has ATPase
activity and belongs to the larger group of P-loop
NTPases. Kinesins are microtubule-dependent molecular
motors that play important roles in intracellular
transport and in cell division. In this group the motor
domain is found at the N-terminus (N-type). N-type
kinesins are (+) end-directed motors, i.e. they
transport cargo towards the (+) end of the microtubule.
Kinesin motor domains hydrolyze ATP at a rate of about
80 per second, and move along the microtubule at a speed
of about 6400 Angstroms per second. To achieve that,
kinesin head groups work in pairs. Upon replacing ADP
with ATP, a kinesin motor domain increases its affinity
for microtubule binding and locks in place. Also, the
neck linker binds to the motor domain, which repositions
the other head domain through the coiled-coil domain
close to a second tubulin dimer, about 80 Angstroms
along the microtubule. Meanwhile, ATP hydrolysis takes
place, and when the second head domain binds to the
microtubule, the first domain again replaces ADP with
ATP, triggering a conformational change that pulls the
first domain forward.
Length = 333
Score = 62.0 bits (151), Expect = 4e-12
Identities = 23/28 (82%), Positives = 24/28 (85%)
Query: 1 MVACLSPADNNYDETLSTLRYANRAKNI 28
M A + PAD NYDETLSTLRYANRAKNI
Sbjct: 306 MCANIGPADYNYDETLSTLRYANRAKNI 333
>gnl|CDD|214526 smart00129, KISc, Kinesin motor, catalytic domain. ATPase.
Microtubule-dependent molecular motors that play
important roles in intracellular transport of organelles
and in cell division.
Length = 335
Score = 61.8 bits (151), Expect = 6e-12
Identities = 21/35 (60%), Positives = 29/35 (82%)
Query: 1 MVACLSPADNNYDETLSTLRYANRAKNIANKPHIN 35
M+A +SP+ +N +ETLSTLR+A+RAK I NKP +N
Sbjct: 301 MIANVSPSSSNLEETLSTLRFASRAKEIKNKPIVN 335
>gnl|CDD|215803 pfam00225, Kinesin, Kinesin motor domain.
Length = 326
Score = 59.5 bits (145), Expect = 3e-11
Identities = 20/28 (71%), Positives = 27/28 (96%)
Query: 1 MVACLSPADNNYDETLSTLRYANRAKNI 28
M+A +SP+D+NY+ETLSTLR+A+RAKNI
Sbjct: 299 MIANISPSDSNYEETLSTLRFASRAKNI 326
>gnl|CDD|238668 cd01372, KISc_KIF4, Kinesin motor domain, KIF4-like subfamily.
Members of this group seem to perform a variety of
functions, and have been implicated in neuronal
organelle transport and chromosome segregation during
mitosis. This catalytic (head) domain has ATPase
activity and belongs to the larger group of P-loop
NTPases. Kinesins are microtubule-dependent molecular
motors that play important roles in intracellular
transport and in cell division. In most kinesins, the
motor domain is found at the N-terminus (N-type). N-type
kinesins are (+) end-directed motors, i.e. they
transport cargo towards the (+) end of the microtubule.
Kinesin motor domains hydrolyze ATP at a rate of about
80 per second, and move along the microtubule at a speed
of about 6400 Angstroms per second. To achieve that,
kinesin head groups work in pairs. Upon replacing ADP
with ATP, a kinesin motor domain increases its affinity
for microtubule binding and locks in place. Also, the
neck linker binds to the motor domain, which repositions
the other head domain through the coiled-coil domain
close to a second tubulin dimer, about 80 Angstroms
along the microtubule. Meanwhile, ATP hydrolysis takes
place, and when the second head domain binds to the
microtubule, the first domain again replaces ADP with
ATP, triggering a conformational change that pulls the
first domain forward.
Length = 341
Score = 58.5 bits (142), Expect = 7e-11
Identities = 20/28 (71%), Positives = 28/28 (100%)
Query: 1 MVACLSPADNNYDETLSTLRYANRAKNI 28
M+AC+SPAD+N++ETL+TL+YANRA+NI
Sbjct: 313 MIACVSPADSNFEETLNTLKYANRARNI 340
>gnl|CDD|238660 cd01364, KISc_BimC_Eg5, Kinesin motor domain, BimC/Eg5 spindle pole
proteins, participate in spindle assembly and chromosome
segregation during cell division. This catalytic (head)
domain has ATPase activity and belongs to the larger
group of P-loop NTPases. Kinesins are
microtubule-dependent molecular motors that play
important roles in intracellular transport and in cell
division. In most kinesins, the motor domain is found at
the N-terminus (N-type), N-type kinesins are (+)
end-directed motors, i.e. they transport cargo towards
the (+) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and move
along the microtubule at a speed of about 6400 Angstroms
per second. To achieve that, kinesin head groups work in
pairs. Upon replacing ADP with ATP, a kinesin motor
domain increases its affinity for microtubule binding
and locks in place. Also, the neck linker binds to the
motor domain, which repositions the other head domain
through the coiled-coil domain close to a second tubulin
dimer, about 80 Angstroms along the microtubule.
Meanwhile, ATP hydrolysis takes place, and when the
second head domain binds to the microtubule, the first
domain again replaces ADP with ATP, triggering a
conformational change that pulls the first domain
forward.
Length = 352
Score = 55.7 bits (135), Expect = 7e-10
Identities = 22/37 (59%), Positives = 29/37 (78%)
Query: 1 MVACLSPADNNYDETLSTLRYANRAKNIANKPHINED 37
++A +SPA N +ETLSTL YA+RAKNI NKP +N+
Sbjct: 316 IIATISPASINLEETLSTLEYAHRAKNIKNKPEVNQK 352
>gnl|CDD|238666 cd01370, KISc_KIP3_like, Kinesin motor domain, KIP3-like subgroup.
The yeast kinesin KIP3 plays a role in positioning the
mitotic spindle. This catalytic (head) domain has ATPase
activity and belongs to the larger group of P-loop
NTPases. Kinesins are microtubule-dependent molecular
motors that play important roles in intracellular
transport and in cell division. In most kinesins, the
motor domain is found at the N-terminus (N-type). N-type
kinesins are (+) end-directed motors, i.e. they
transport cargo towards the (+) end of the microtubule.
Kinesin motor domains hydrolyze ATP at a rate of about
80 per second, and move along the microtubule at a speed
of about 6400 Angstroms per second. To achieve that,
kinesin head groups work in pairs. Upon replacing ADP
with ATP, a kinesin motor domain increases its affinity
for microtubule binding and locks in place. Also, the
neck linker binds to the motor domain, which repositions
the other head domain through the coiled-coil domain
close to a second tubulin dimer, about 80 Angstroms
along the microtubule. Meanwhile, ATP hydrolysis takes
place, and when the second head domain binds to the
microtubule, the first domain again replaces ADP with
ATP, triggering a conformational change that pulls the
first domain forward.
Length = 338
Score = 52.3 bits (126), Expect = 1e-08
Identities = 17/28 (60%), Positives = 25/28 (89%)
Query: 1 MVACLSPADNNYDETLSTLRYANRAKNI 28
M+A +SP+ ++Y+ET +TL+YANRAKNI
Sbjct: 311 MIANISPSSSHYEETHNTLKYANRAKNI 338
>gnl|CDD|238054 cd00106, KISc, Kinesin motor domain. This catalytic (head) domain
has ATPase activity and belongs to the larger group of
P-loop NTPases. Kinesins are microtubule-dependent
molecular motors that play important roles in
intracellular transport and in cell division. In most
kinesins, the motor domain is found at the N-terminus
(N-type), in some its is found in the middle (M-type),
or C-terminal (C-type). N-type and M-type kinesins are
(+) end-directed motors, while C-type kinesins are (-)
end-directed motors, i.e. they transport cargo towards
the (-) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and move
along the microtubule at a speed of about 6400 Angstroms
per second. To achieve that, kinesin head groups work in
pairs. Upon replacing ADP with ATP, a kinesin motor
domain increases its affinity for microtubule binding
and locks in place. Also, the neck linker binds to the
motor domain, which repositions the other head domain
through the coiled-coil domain close to a second tubulin
dimer, about 80 Angstroms along the microtubule.
Meanwhile, ATP hydrolysis takes place, and when the
second head domain binds to the microtubule, the first
domain again replaces ADP with ATP, triggering a
conformational change that pulls the first domain
forward.
Length = 328
Score = 49.5 bits (119), Expect = 1e-07
Identities = 18/26 (69%), Positives = 23/26 (88%)
Query: 1 MVACLSPADNNYDETLSTLRYANRAK 26
M+A +SP+ NYDETLSTLR+A+RAK
Sbjct: 303 MIANISPSSENYDETLSTLRFASRAK 328
>gnl|CDD|227392 COG5059, KIP1, Kinesin-like protein [Cytoskeleton].
Length = 568
Score = 49.7 bits (119), Expect = 1e-07
Identities = 29/138 (21%), Positives = 58/138 (42%), Gaps = 10/138 (7%)
Query: 1 MVACLSPADNNYDETLSTLRYANRAKNIANKPHINEDPKDTMLREYQEEIRQLRALLESS 60
++ +SP+ N+++ET++TL++A+RAK+I NK +N + EEI+ + S
Sbjct: 309 VICTISPSSNSFEETINTLKFASRAKSIKNKIQVNSSSDSSR---EIEEIKFDLSEDRSE 365
Query: 61 GSVPLSGGVCMMNSSSAMDSTTPLEKEKLRLEYEAEMEKLREQYNAERNSK-SKMEADLQ 119
+ + S S++ + E E L+ + + S S +
Sbjct: 366 IEILVFRE-QSQLSQSSLS-----GIFAYMQSLKKETETLKSRIDLIMKSIISGTFERKK 419
Query: 120 ALKEQYQRDMENIGNNNS 137
LKE+ + +
Sbjct: 420 LLKEEGWKYKSTLQFLRI 437
>gnl|CDD|215621 PLN03188, PLN03188, kinesin-12 family protein; Provisional.
Length = 1320
Score = 45.7 bits (108), Expect = 3e-06
Identities = 28/56 (50%), Positives = 35/56 (62%), Gaps = 5/56 (8%)
Query: 1 MVACLSPADNNYDETLSTLRYANRAKNIANKPHINEDPKDTM--LREYQEEIRQLR 54
MV +SP+ + ET STLR+A RAK I NK +NE +D + LRE IRQLR
Sbjct: 407 MVCAISPSQSCKSETFSTLRFAQRAKAIKNKAVVNEVMQDDVNFLREV---IRQLR 459
>gnl|CDD|238663 cd01367, KISc_KIF2_like, Kinesin motor domain, KIF2-like group.
KIF2 is a protein expressed in neurons, which has been
associated with axonal transport and neuron development;
alternative splice forms have been implicated in
lysosomal translocation. This catalytic (head) domain
has ATPase activity and belongs to the larger group of
P-loop NTPases. Kinesins are microtubule-dependent
molecular motors that play important roles in
intracellular transport and in cell division. In this
subgroup the motor domain is found in the middle
(M-type) of the protein chain. M-type kinesins are (+)
end-directed motors, i.e. they transport cargo towards
the (+) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and move
along the microtubule at a speed of about 6400 Angstroms
per second (KIF2 may be slower). To achieve that,
kinesin head groups work in pairs. Upon replacing ADP
with ATP, a kinesin motor domain increases its affinity
for microtubule binding and locks in place. Also, the
neck linker binds to the motor domain, which repositions
the other head domain through the coiled-coil domain
close to a second tubulin dimer, about 80 Angstroms
along the microtubule. Meanwhile, ATP hydrolysis takes
place, and when the second head domain binds to the
microtubule, the first domain again replaces ADP with
ATP, triggering a conformational change that pulls the
first domain forward.
Length = 322
Score = 41.9 bits (99), Expect = 4e-05
Identities = 13/26 (50%), Positives = 21/26 (80%)
Query: 1 MVACLSPADNNYDETLSTLRYANRAK 26
M+A +SP+ ++ + TL+TLRYA+R K
Sbjct: 297 MIATISPSASSCEHTLNTLRYADRVK 322
>gnl|CDD|238665 cd01369, KISc_KHC_KIF5, Kinesin motor domain, kinesin heavy chain
(KHC) or KIF5-like subgroup. Members of this group have
been associated with organelle transport. This catalytic
(head) domain has ATPase activity and belongs to the
larger group of P-loop NTPases. Kinesins are
microtubule-dependent molecular motors that play
important roles in intracellular transport and in cell
division. In most kinesins, the motor domain is found at
the N-terminus (N-type). N-type kinesins are (+)
end-directed motors, i.e. they transport cargo towards
the (+) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and move
along the microtubule at a speed of about 6400 Angstroms
per second. To achieve that, kinesin head groups work in
pairs. Upon replacing ADP with ATP, a kinesin motor
domain increases its affinity for microtubule binding
and locks in place. Also, the neck linker binds to the
motor domain, which repositions the other head domain
through the coiled-coil domain close to a second tubulin
dimer, about 80 Angstroms along the microtubule.
Meanwhile, ATP hydrolysis takes place, and when the
second head domain binds to the microtubule, the first
domain again replaces ADP with ATP, triggering a
conformational change that pulls the first domain
forward.
Length = 325
Score = 41.5 bits (98), Expect = 6e-05
Identities = 15/28 (53%), Positives = 19/28 (67%)
Query: 1 MVACLSPADNNYDETLSTLRYANRAKNI 28
++ C SP+ N ETLSTLR+ RAK I
Sbjct: 298 LIICCSPSSYNESETLSTLRFGARAKTI 325
>gnl|CDD|238662 cd01366, KISc_C_terminal, Kinesin motor domain,
KIFC2/KIFC3/ncd-like carboxy-terminal kinesins. Ncd is a
spindle motor protein necessary for chromosome
segregation in meiosis. KIFC2/KIFC3-like kinesins have
been implicated in motility of the Golgi apparatus as
well as dentritic and axonal transport in neurons. This
catalytic (head) domain has ATPase activity and belongs
to the larger group of P-loop NTPases. Kinesins are
microtubule-dependent molecular motors that play
important roles in intracellular transport and in cell
division. In this subgroup the motor domain is found at
the C-terminus (C-type). C-type kinesins are (-)
end-directed motors, i.e. they transport cargo towards
the (-) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and move
along the microtubule at a speed of about 6400 Angstroms
per second. To achieve that, kinesin head groups work in
pairs. Upon replacing ADP with ATP, a kinesin motor
domain increases its affinity for microtubule binding
and locks in place. Also, the neck linker binds to the
motor domain, which repositions the other head domain
through the coiled-coil domain close to a second tubulin
dimer, about 80 Angstroms along the microtubule.
Meanwhile, ATP hydrolysis takes place, and when the
second head domain binds to the microtubule, the first
domain again replaces ADP with ATP, triggering a
conformational change that pulls the first domain
forward.
Length = 329
Score = 38.7 bits (91), Expect = 5e-04
Identities = 11/30 (36%), Positives = 20/30 (66%)
Query: 1 MVACLSPADNNYDETLSTLRYANRAKNIAN 30
M +SP ++N ETL +LR+A+R +++
Sbjct: 299 MFVNISPLESNLSETLCSLRFASRVRSVEL 328
>gnl|CDD|238670 cd01374, KISc_CENP_E, Kinesin motor domain, CENP-E/KIP2-like
subgroup, involved in chromosome movement and/or spindle
elongation during mitosis. This catalytic (head) domain
has ATPase activity and belongs to the larger group of
P-loop NTPases. Kinesins are microtubule-dependent
molecular motors that play important roles in
intracellular transport and in cell division. In most
kinesins, the motor domain is found at the N-terminus
(N-type). N-type kinesins are (+) end-directed motors,
i.e. they transport cargo towards the (+) end of the
microtubule. Kinesin motor domains hydrolyze ATP at a
rate of about 80 per second, and move along the
microtubule at a speed of about 6400 Angstroms per
second. To achieve that, kinesin head groups work in
pairs. Upon replacing ADP with ATP, a kinesin motor
domain increases its affinity for microtubule binding
and locks in place. Also, the neck linker binds to the
motor domain, which repositions the other head domain
through the coiled-coil domain close to a second tubulin
dimer, about 80 Angstroms along the microtubule.
Meanwhile, ATP hydrolysis takes place, and when the
second head domain binds to the microtubule, the first
domain again replaces ADP with ATP, triggering a
conformational change that pulls the first domain
forward.
Length = 321
Score = 36.9 bits (86), Expect = 0.002
Identities = 12/24 (50%), Positives = 21/24 (87%)
Query: 5 LSPADNNYDETLSTLRYANRAKNI 28
+SPA ++ +ETL+TL++A+RAK +
Sbjct: 298 ISPASSHVEETLNTLKFASRAKKV 321
>gnl|CDD|234252 TIGR03545, TIGR03545, TIGR03545 family protein. This model
represents a relatively rare but broadly distributed
uncharacterized protein family, distributed in 1-2
percent of bacterial genomes, all of which have outer
membranes. In many of these genomes, it is part of a
two-gene pair.
Length = 555
Score = 35.5 bits (82), Expect = 0.007
Identities = 20/65 (30%), Positives = 38/65 (58%)
Query: 85 EKEKLRLEYEAEMEKLREQYNAERNSKSKMEADLQALKEQYQRDMENIGNNNSINTGSTD 144
E +KL+ E +A+ +K++ N +N K +++ADL LK+ Q D++ + N +I +G
Sbjct: 220 EFDKLKKEGKADKQKIKSAKNDLQNDKKQLKADLAELKKAPQNDLKRLENKYAIKSGDLK 279
Query: 145 ILSTD 149
+ D
Sbjct: 280 NFAVD 284
>gnl|CDD|238671 cd01375, KISc_KIF9_like, Kinesin motor domain, KIF9-like subgroup;
might play a role in cell shape remodeling. This
catalytic (head) domain has ATPase activity and belongs
to the larger group of P-loop NTPases. Kinesins are
microtubule-dependent molecular motors that play
important roles in intracellular transport and in cell
division. In most kinesins, the motor domain is found at
the N-terminus (N-type). N-type kinesins are (+)
end-directed motors, i.e. they transport cargo towards
the (+) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and move
along the microtubule at a speed of about 6400 Angstroms
per second. To achieve that, kinesin head groups work in
pairs. Upon replacing ADP with ATP, a kinesin motor
domain increases its affinity for microtubule binding
and locks in place. Also, the neck linker binds to the
motor domain, which repositions the other head domain
through the coiled-coil domain close to a second tubulin
dimer, about 80 Angstroms along the microtubule.
Meanwhile, ATP hydrolysis takes place, and when the
second head domain binds to the microtubule, the first
domain again replaces ADP with ATP, triggering a
conformational change that pulls the first domain
forward.
Length = 334
Score = 34.4 bits (79), Expect = 0.014
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 1 MVACLSPADNNYDETLSTLRYANRAK 26
M+A + +N DETLSTLR+A R
Sbjct: 309 MLATIWVEPSNLDETLSTLRFAQRVA 334
>gnl|CDD|238669 cd01373, KISc_KLP2_like, Kinesin motor domain, KLP2-like subgroup.
Members of this subgroup seem to play a role in mitosis
and meiosis. This catalytic (head) domain has ATPase
activity and belongs to the larger group of P-loop
NTPases. Kinesins are microtubule-dependent molecular
motors that play important roles in intracellular
transport and in cell division. In most kinesins, the
motor domain is found at the N-terminus (N-type). N-type
kinesins are (+) end-directed motors, i.e. they
transport cargo towards the (+) end of the microtubule.
Kinesin motor domains hydrolyze ATP at a rate of about
80 per second, and move along the microtubule at a speed
of about 6400 Angstroms per second. To achieve that,
kinesin head groups work in pairs. Upon replacing ADP
with ATP, a kinesin motor domain increases its affinity
for microtubule binding and locks in place. Also, the
neck linker binds to the motor domain, which repositions
the other head domain through the coiled-coil domain
close to a second tubulin dimer, about 80 Angstroms
along the microtubule. Meanwhile, ATP hydrolysis takes
place, and when the second head domain binds to the
microtubule, the first domain again replaces ADP with
ATP, triggering a conformational change that pulls the
first domain forward.
Length = 337
Score = 32.8 bits (75), Expect = 0.046
Identities = 14/28 (50%), Positives = 21/28 (75%)
Query: 1 MVACLSPADNNYDETLSTLRYANRAKNI 28
++A +SP+ + ETLSTL++A RAK I
Sbjct: 310 IIANVSPSSKCFGETLSTLKFAQRAKLI 337
>gnl|CDD|220369 pfam09731, Mitofilin, Mitochondrial inner membrane protein.
Mitofilin controls mitochondrial cristae morphology.
Mitofilin is enriched in the narrow space between the
inner boundary and the outer membranes, where it forms a
homotypic interaction and assembles into a large
multimeric protein complex. The first 78 amino acids
contain a typical amino-terminal-cleavable mitochondrial
presequence rich in positive-charged and hydroxylated
residues and a membrane anchor domain. In addition, it
has three centrally located coiled coil domains.
Length = 493
Score = 32.3 bits (74), Expect = 0.081
Identities = 14/52 (26%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 75 SSAMDSTTPLEKEKLRLEYEAEMEKLREQYNAERNSKSKMEADLQALKEQYQ 126
+ ++S +++LRLE+E E E+LR++Y K+ +L+ E ++
Sbjct: 210 LARLESKEAALEKQLRLEFEREKEELRKKYE------EKLRQELERQAEAHE 255
>gnl|CDD|234201 TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase. Members of
this protein family are hydroxyacylglutathione
hydrolase, a detoxification enzyme known as glyoxalase
II. It follows lactoylglutathione lyase, or glyoxalase
I, and acts to remove the toxic metabolite methylglyoxal
and related compounds. This protein belongs to the
broader metallo-beta-lactamase family (pfam00753)
[Cellular processes, Detoxification].
Length = 248
Score = 31.7 bits (73), Expect = 0.099
Identities = 13/41 (31%), Positives = 20/41 (48%), Gaps = 11/41 (26%)
Query: 15 TLSTLRYANRAKNIANKPHINEDPKDTMLREYQEEIRQLRA 55
TLS LR+A + +P + L+E +E+ LRA
Sbjct: 167 TLSNLRFAL---------TV--EPDNPALQERLKEVEALRA 196
>gnl|CDD|240439 PTZ00491, PTZ00491, major vault protein; Provisional.
Length = 850
Score = 31.9 bits (73), Expect = 0.13
Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 12/62 (19%)
Query: 82 TPLEKEKLRLEYEAEMEKLRE------QYNAERNS----KSKMEADLQALKEQYQRDMEN 131
L + LR+E EAE+EKLR+ +Y +N K+K AD++A +++R +E
Sbjct: 739 AELRAKALRIEAEAELEKLRKRQELELEYEQAQNELEIAKAKELADIEA--TKFERIVEA 796
Query: 132 IG 133
+G
Sbjct: 797 LG 798
>gnl|CDD|238664 cd01368, KISc_KIF23_like, Kinesin motor domain, KIF23-like
subgroup. Members of this group may play a role in
mitosis. This catalytic (head) domain has ATPase
activity and belongs to the larger group of P-loop
NTPases. Kinesins are microtubule-dependent molecular
motors that play important roles in intracellular
transport and in cell division. In most kinesins, the
motor domain is found at the N-terminus (N-type). N-type
kinesins are (+) end-directed motors, i.e. they
transport cargo towards the (+) end of the microtubule.
Kinesin motor domains hydrolyze ATP at a rate of about
80 per second, and move along the microtubule at a speed
of about 6400 Angstroms per second. To achieve that,
kinesin head groups work in pairs. Upon replacing ADP
with ATP, a kinesin motor domain increases its affinity
for microtubule binding and locks in place. Also, the
neck linker binds to the motor domain, which repositions
the other head domain through the coiled-coil domain
close to a second tubulin dimer, about 80 Angstroms
along the microtubule. Meanwhile, ATP hydrolysis takes
place, and when the second head domain binds to the
microtubule, the first domain again replaces ADP with
ATP, triggering a conformational change that pulls the
first domain forward.
Length = 345
Score = 31.2 bits (71), Expect = 0.17
Identities = 8/26 (30%), Positives = 18/26 (69%)
Query: 1 MVACLSPADNNYDETLSTLRYANRAK 26
M+ ++P ++YDETL ++++ A+
Sbjct: 320 MIVNVNPCASDYDETLHVMKFSAIAQ 345
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 30.1 bits (69), Expect = 0.41
Identities = 14/50 (28%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 84 LEKEKLRLEY-EAEMEKLREQYNAERNSKSKMEADLQALKEQYQRDMENI 132
L+++ LE E E+EK ++ ++ K E +L+ L E+ +++E I
Sbjct: 98 LDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEELIEEQLQELERI 147
>gnl|CDD|217817 pfam03961, DUF342, Protein of unknown function (DUF342). This
family of bacterial proteins has no known function. The
proteins are in the region of 500-600 amino acid
residues in length.
Length = 450
Score = 30.3 bits (69), Expect = 0.44
Identities = 19/101 (18%), Positives = 39/101 (38%), Gaps = 14/101 (13%)
Query: 43 LREYQEEIRQLRALLESSGSVPLSGGVCMMNSSSAMDSTTPLEKEKLRLEYEAEMEKLRE 102
L+E +E+ + LE + + + +L E ++EKL E
Sbjct: 332 LKEELKELEEELKELEEE----------LEKIKKLLKKLPKKARGQLPPEKREQLEKLLE 381
Query: 103 QYNAERNSKSKMEADLQALKEQYQRDMENIGNNNSINTGST 143
++E +L+ LKE+ +E++ + I+ T
Sbjct: 382 TKEKLSEELEELEEELKELKEE----LESLYSEGKISVNKT 418
>gnl|CDD|238672 cd01376, KISc_KID_like, Kinesin motor domain, KIF22/Kid-like
subgroup. Members of this group might play a role in
regulating chromosomal movement along microtubules in
mitosis. This catalytic (head) domain has ATPase
activity and belongs to the larger group of P-loop
NTPases. Kinesins are microtubule-dependent molecular
motors that play important roles in intracellular
transport and in cell division. In most kinesins, the
motor domain is found at the N-terminus (N-type). N-type
kinesins are (+) end-directed motors, i.e. they
transport cargo towards the (+) end of the microtubule.
Kinesin motor domains hydrolyze ATP at a rate of about
80 per second, and move along the microtubule at a speed
of about 6400 Angstroms per second. To achieve that,
kinesin head groups work in pairs. Upon replacing ADP
with ATP, a kinesin motor domain increases its affinity
for microtubule binding and locks in place. Also, the
neck linker binds to the motor domain, which repositions
the other head domain through the coiled-coil domain
close to a second tubulin dimer, about 80 Angstroms
along the microtubule. Meanwhile, ATP hydrolysis takes
place, and when the second head domain binds to the
microtubule, the first domain again replaces ADP with
ATP, triggering a conformational change that pulls the
first domain forward.
Length = 319
Score = 30.1 bits (68), Expect = 0.48
Identities = 13/26 (50%), Positives = 20/26 (76%)
Query: 1 MVACLSPADNNYDETLSTLRYANRAK 26
MVA ++P + Y +TLSTL +A+R+K
Sbjct: 294 MVANIAPERSFYQDTLSTLNFASRSK 319
>gnl|CDD|239013 cd02058, PAI-2, Plasminogen Activator Inhibitor-2 (PAI-2). PAI-2 is
a serine protease inhibitor that belongs to the
ov-serpin branch of the serpin superfamily. It is is an
effective inhibitor of urinary plasminogen activator
(urokinase or uPA) and is involved in cell
differentiation, tissue growth and regeneration.
Length = 380
Score = 29.3 bits (66), Expect = 0.72
Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 8/70 (11%)
Query: 79 DSTTPLEKEKLRLEYEAEMEKLREQYNAERNSKSKMEADLQALKEQYQRDME----NIGN 134
D TT LEK LE E EKL E + E + ++E L K + D++ ++G
Sbjct: 239 DVTTGLEK----LEKELTYEKLNEWTSPEMMEEYEVEVYLPKFKLEESYDLKSTLSSMGM 294
Query: 135 NNSINTGSTD 144
++ + G D
Sbjct: 295 EDAFDPGKAD 304
>gnl|CDD|220664 pfam10267, Tmemb_cc2, Predicted transmembrane and coiled-coil 2
protein. This family of transmembrane coiled-coil
containing proteins is conserved from worms to humans.
Its function is unknown.
Length = 387
Score = 29.4 bits (66), Expect = 0.73
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 2/63 (3%)
Query: 72 MNSSSAMDSTTPLEKEKLRLEYEAE--MEKLREQYNAERNSKSKMEADLQALKEQYQRDM 129
SSSA ++ + + ++KL E+ + +S++E + LKEQ QRD
Sbjct: 180 ATSSSAGANSNSGSGPGSAVAQQQSLNLDKLLEELREIKEGQSRLEESYERLKEQLQRDY 239
Query: 130 ENI 132
+ I
Sbjct: 240 QYI 242
>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 = 28.8 bits (65), Expect = 0.90
Identities = 9/42 (21%), Positives = 20/42 (47%), Gaps = 3/42 (7%)
Query: 92 EYEAEMEKLREQYNAERNSKSKMEADLQALKEQYQRDMENIG 133
+ ++EK ++ AE K E +LQ +++ Q+ +
Sbjct: 35 AAQKQLEKEFKKLQAELQ---KKEKELQKEEQKLQKQAATLS 73
Score = 27.2 bits (61), Expect = 2.5
Identities = 10/53 (18%), Positives = 25/53 (47%), Gaps = 8/53 (15%)
Query: 87 EKLRLEYEAEMEKLR--------EQYNAERNSKSKMEADLQALKEQYQRDMEN 131
+K E + E +KL+ E A++ + + +LQ ++ Q++++
Sbjct: 52 QKKEKELQKEEQKLQKQAATLSEEARKAKQQELQQKQQELQQKQQAAQQELQQ 104
>gnl|CDD|234820 PRK00714, PRK00714, RNA pyrophosphohydrolase; Reviewed.
Length = 156
Score = 28.6 bits (65), Expect = 0.91
Identities = 7/16 (43%), Positives = 9/16 (56%)
Query: 35 NEDPKDTMLREYQEEI 50
E P+ M RE EE+
Sbjct: 44 GETPEQAMYRELYEEV 59
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial 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. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 29.3 bits (66), Expect = 0.94
Identities = 23/99 (23%), Positives = 40/99 (40%), Gaps = 6/99 (6%)
Query: 43 LREYQEEIRQLRALLESSGSVPLSGGVCMMNSSSAMD--STTPLEKEKLRLEYEAEMEKL 100
+ E +E I +L + LE+ + S + S ++ S E E R E E+E+L
Sbjct: 861 IEELEELIEELESELEALLNERASLEEALALLRSELEELSEELRELESKRSELRRELEEL 920
Query: 101 REQYNAERNSKSKMEADLQALKEQ----YQRDMENIGNN 135
RE+ +E + L+E+ Y +E
Sbjct: 921 REKLAQLELRLEGLEVRIDNLQERLSEEYSLTLEEAEAL 959
>gnl|CDD|239643 cd03671, Ap4A_hydrolase_plant_like, Diadenosine tetraphosphate
(Ap4A) hydrolase is a member of the Nudix hydrolase
superfamily. Members of this family are well
represented in a variety of prokaryotic and eukaryotic
organisms. Phylogenetic analysis reveals two distinct
subgroups where plant enzymes fall into one group
(represented by this subfamily) and
fungi/animals/archaea enzymes fall into another.
Bacterial enzymes are found in both subfamilies. Ap4A
is a potential by-product of aminoacyl tRNA synthesis,
and accumulation of Ap4A has been implicated in a range
of biological events, such as DNA replication, cellular
differentiation, heat shock, metabolic stress, and
apoptosis. Ap4A hydrolase cleaves Ap4A asymmetrically
into ATP and AMP. It is important in the invasive
properties of bacteria and thus presents a potential
target for the inhibition of such invasive bacteria.
Besides the signature nudix motif (G[X5]E[X7]REUXEEXGU
where U is Ile, Leu, or Val), Ap4A hydrolase is
structurally similar to the other members of the nudix
superfamily with some degree of variations. Several
regions in the sequences are poorly defined and
substrate and metal binding sites are only predicted
based on kinetic studies.
Length = 147
Score = 27.9 bits (63), Expect = 1.3
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 35 NEDPKDTMLREYQEEI 50
EDP+ LRE +EE
Sbjct: 39 GEDPEQAALRELEEET 54
>gnl|CDD|200948 pfam00038, Filament, Intermediate filament protein.
Length = 312
Score = 28.3 bits (64), Expect = 1.5
Identities = 20/82 (24%), Positives = 34/82 (41%), Gaps = 25/82 (30%)
Query: 46 YQEEIRQLRALLESSGSVPLSGGVCMMNSSSAMDSTTPLEKEKLRLEYE---AEMEKLRE 102
Y++EIR+LR L+ + E+ +L+LE + E RE
Sbjct: 52 YEQEIRELRKQLDELTN----------------------ERARLQLEIDNLRLAAEDFRE 89
Query: 103 QYNAERNSKSKMEADLQALKEQ 124
+Y E N + E D+ L++
Sbjct: 90 KYEDELNLRQSAENDIVGLRKD 111
>gnl|CDD|235316 PRK04863, mukB, cell division protein MukB; Provisional.
Length = 1486
Score = 28.8 bits (65), Expect = 1.6
Identities = 14/47 (29%), Positives = 23/47 (48%)
Query: 81 TTPLEKEKLRLEYEAEMEKLREQYNAERNSKSKMEADLQALKEQYQR 127
E E+L+ E EA +E L E + R + + L+ L+ + QR
Sbjct: 551 DDEDELEQLQEELEARLESLSESVSEARERRMALRQQLEQLQARIQR 597
>gnl|CDD|148614 pfam07106, TBPIP, Tat binding protein 1(TBP-1)-interacting protein
(TBPIP). This family consists of several eukaryotic
TBP-1 interacting protein (TBPIP) sequences. TBP-1 has
been demonstrated to interact with the human
immunodeficiency virus type 1 (HIV-1) viral protein Tat,
then modulate the essential replication process of HIV.
In addition, TBP-1 has been shown to be a component of
the 26S proteasome, a basic multiprotein complex that
degrades ubiquitinated proteins in an ATP-dependent
fashion. Human TBPIP interacts with human TBP-1 then
modulates the inhibitory action of human TBP-1 on
HIV-Tat-mediated transactivation.
Length = 169
Score = 28.0 bits (63), Expect = 1.6
Identities = 21/105 (20%), Positives = 38/105 (36%), Gaps = 21/105 (20%)
Query: 36 EDPKDTMLREYQEEIRQLRALLESSGSVPLSGGVCMMNSSSAMDSTTPLEKEKLRLEYEA 95
E P D L + EI +LR ++ + LE E L +
Sbjct: 67 ELPSDEELNKLDMEIEELREEVQLLK-----------------QDCSTLEIELKSLTSDL 109
Query: 96 EMEKLREQYNAERNSKSKMEADLQALKE----QYQRDMENIGNNN 136
E+L+E+ + ++E L++L+E +ME +
Sbjct: 110 TTEELQEEIQELKKEVREIEEKLESLEEGWKPVTPEEMEKVKKEY 154
>gnl|CDD|240046 cd04690, Nudix_Hydrolase_31, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent
cation, such as Mg2+ or Mn2+, for their activity and
contain a highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. Substrates of
nudix hydrolases include intact and oxidatively damaged
nucleoside triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the
nucleotide pools and to maintain cell viability,
thereby serving as surveillance & "house-cleaning"
enzymes. Substrate specificity is used to define
families within the superfamily. Differences in
substrate specificity are determined by the N-terminal
extension or by residues in variable loop regions.
Mechanistically, substrate hydrolysis occurs by a
nucleophilic substitution reaction, with variation in
the numbers and roles of divalent cations required.
Length = 118
Score = 27.6 bits (62), Expect = 1.7
Identities = 7/21 (33%), Positives = 10/21 (47%)
Query: 31 KPHINEDPKDTMLREYQEEIR 51
K E P ++RE EE+
Sbjct: 31 KIEAGETPLQALIRELSEELG 51
>gnl|CDD|222281 pfam13641, Glyco_tranf_2_3, Glycosyltransferase like family 2.
Members of this family of prokaryotic proteins include
putative glucosyltransferase, which are involved in
bacterial capsule biosynthesis.
Length = 229
Score = 28.1 bits (63), Expect = 1.9
Identities = 16/88 (18%), Positives = 26/88 (29%), Gaps = 6/88 (6%)
Query: 45 EYQEEIRQLRALLESSGSVPLSGGVCMMNSSSAMDSTTPLEKEKLR-----LEYEAEMEK 99
E+ + AL + G PL+G + S ++ + L L
Sbjct: 139 EFALRHLRFMALRRALGVAPLAGSGSLF-RRSVLEEIGGFDPGFLLGEDKELGLRLRRAG 197
Query: 100 LREQYNAERNSKSKMEADLQALKEQYQR 127
R Y + L A +Q R
Sbjct: 198 WRTAYVPGAAVYELSPSSLAAFIKQRTR 225
>gnl|CDD|214922 smart00935, 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 = 140
Score = 27.5 bits (62), Expect = 1.9
Identities = 11/40 (27%), Positives = 22/40 (55%)
Query: 92 EYEAEMEKLREQYNAERNSKSKMEADLQALKEQYQRDMEN 131
+A ++L +++ + K+E +LQ LKE+ Q+D
Sbjct: 15 AGKAAQKQLEKEFKKRQAELEKLEKELQKLKEKLQKDAAT 54
Score = 26.8 bits (60), Expect = 3.6
Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 10/72 (13%)
Query: 70 CMMNSSSAMDSTTPLEKE--KLRLEY---EAEMEKLREQYNAERNS-----KSKMEADLQ 119
+ S + + LEKE K + E E E++KL+E+ + + + K E +LQ
Sbjct: 9 ILQESPAGKAAQKQLEKEFKKRQAELEKLEKELQKLKEKLQKDAATLSEAAREKKEKELQ 68
Query: 120 ALKEQYQRDMEN 131
+++QR +
Sbjct: 69 KKVQEFQRKQQK 80
>gnl|CDD|235582 PRK05729, valS, valyl-tRNA synthetase; Reviewed.
Length = 874
Score = 28.1 bits (64), Expect = 2.0
Identities = 10/20 (50%), Positives = 16/20 (80%), Gaps = 1/20 (5%)
Query: 85 EKEKLRL-EYEAEMEKLREQ 103
EKE+ +L EYE ++ KL+E+
Sbjct: 849 EKEREKLAEYEEKLAKLKER 868
>gnl|CDD|100050 cd03360, LbH_AT_putative, Putative Acyltransferase (AT),
Left-handed parallel beta-Helix (LbH) domain; This group
is composed of mostly uncharacterized proteins
containing an N-terminal helical subdomain followed by a
LbH domain. The alignment contains 6 turns, each
containing three imperfect tandem repeats of a
hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X).
Proteins containing hexapeptide repeats are often
enzymes showing acyltransferase activity. A few members
are identified as NeuD, a sialic acid (Sia)
O-acetyltransferase that is required for Sia synthesis
and surface polysaccharide sialylation.
Length = 197
Score = 27.8 bits (63), Expect = 2.2
Identities = 7/12 (58%), Positives = 9/12 (75%)
Query: 132 IGNNNSINTGST 143
IG+N INTG+
Sbjct: 117 IGDNVIINTGAV 128
>gnl|CDD|226809 COG4372, COG4372, Uncharacterized protein conserved in bacteria
with the myosin-like domain [Function unknown].
Length = 499
Score = 28.1 bits (62), Expect = 2.4
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 3/53 (5%)
Query: 85 EKEKLRLEYEA---EMEKLREQYNAERNSKSKMEADLQALKEQYQRDMENIGN 134
E+E R E + E E +R++ A R + +K + +L L +Q Q +
Sbjct: 103 EREAARSELQKARQEREAVRQELAAARQNLAKAQQELARLTKQAQDLQTRLKT 155
>gnl|CDD|191111 pfam04849, HAP1_N, HAP1 N-terminal conserved region. This family
represents an N-terminal conserved region found in
several huntingtin-associated protein 1 (HAP1)
homologues. HAP1 binds to huntingtin in a polyglutamine
repeat-length-dependent manner. However, its possible
role in the pathogenesis of Huntington's disease is
unclear. This family also includes a similar N-terminal
conserved region from hypothetical protein products of
ALS2CR3 genes found in the human juvenile amyotrophic
lateral sclerosis critical region 2q33-2q34.
Length = 307
Score = 27.9 bits (62), Expect = 2.5
Identities = 12/41 (29%), Positives = 27/41 (65%)
Query: 92 EYEAEMEKLREQYNAERNSKSKMEADLQALKEQYQRDMENI 132
Y E E+L++ A ++++ +++A+LQ L+++Y ME +
Sbjct: 253 SYALENEELQQHLAAAKDAQRQLQAELQELQDKYAECMEML 293
>gnl|CDD|239518 cd03426, CoAse, Coenzyme A pyrophosphatase (CoAse), a member of
the Nudix hydrolase superfamily, functions to catalyze
the elimination of oxidized inactive CoA, which can
inhibit CoA-utilizing enzymes. The need of CoAses
mainly arises under conditions of oxidative stress.
CoAse has a conserved Nudix fold and requires a single
divalent cation for catalysis. In addition to a
signature Nudix motif G[X5]E[X7]REUXEEXGU, where U is
Ile, Leu, or Val, CoAse contains an additional motif
upstream called the NuCoA motif (LLTXT(SA)X3RX3GX3FPGG)
which is postulated to be involved in CoA recognition.
CoA plays a central role in lipid metabolism. It is
involved in the initial steps of fatty acid sythesis in
the cytosol, in the oxidation of fatty acids and the
citric acid cycle in the mitochondria, and in the
oxidation of long-chain fatty acids in peroxisomes. CoA
has the important role of activating fatty acids for
further modification into key biological signalling
molecules.
Length = 157
Score = 27.1 bits (61), Expect = 2.8
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 36 EDPKDTMLREYQEEI 50
EDP T LRE +EEI
Sbjct: 46 EDPVATALREAEEEI 60
>gnl|CDD|168472 PRK06217, PRK06217, hypothetical protein; Validated.
Length = 183
Score = 27.3 bits (61), Expect = 3.2
Identities = 24/83 (28%), Positives = 32/83 (38%), Gaps = 21/83 (25%)
Query: 32 PHINED-----PKD---TMLREYQEEIRQLRALLESSGSVPLSGGVCMMNSSSAMDSTTP 83
PH++ D P D T R +E +R L L LSG SA+ P
Sbjct: 28 PHLDTDDYFWLPTDPPFTTKRPPEERLRLLLEDLRPREGWVLSG--------SALGWGDP 79
Query: 84 LEKEK-----LRLEYEAEMEKLR 101
LE L + E +E+LR
Sbjct: 80 LEPLFDLVVFLTIPPELRLERLR 102
>gnl|CDD|235502 PRK05560, PRK05560, DNA gyrase subunit A; Validated.
Length = 805
Score = 27.7 bits (63), Expect = 3.5
Identities = 12/48 (25%), Positives = 24/48 (50%), Gaps = 5/48 (10%)
Query: 82 TPLEKEKLRLEYEAEMEKLREQYNAERNSKSK----MEADLQALKEQY 125
T LE++K+ EY+ E+ L S + ++ +L +KE++
Sbjct: 428 TGLERDKIEDEYK-ELLALIADLKDILASPERLLEIIKEELLEIKEKF 474
>gnl|CDD|179508 PRK02944, PRK02944, OxaA-like protein precursor; Validated.
Length = 255
Score = 27.0 bits (60), Expect = 3.8
Identities = 12/55 (21%), Positives = 29/55 (52%), Gaps = 13/55 (23%)
Query: 72 MNSSSAMDSTTPLEKEKLRLEYEAEMEKLREQYNA-ERNSKSKMEADLQALKEQY 125
S+ AM + P EM+KL+E+Y++ ++ ++ K++ ++ L ++
Sbjct: 82 TKSTKAMQALQP------------EMQKLKEKYSSKDQATQQKLQQEMMQLFQKN 124
>gnl|CDD|131216 TIGR02161, napC_nirT, periplasmic nitrate (or nitrite) reductase
c-type cytochrome, NapC/NirT family. Nearly every
member of this subfamily is NapC, a predicted
membrane-anchored four-heme c-type cytochrome that
forms one component of the periplasmic nitrate
reductase along with NapA, NapB, NapD, NapE, and NapF
subunits. A single known exception at this time is
NirT, which is instead a component of a nitrite
reductase. This family excludes TorC subunits of
trimethylamine N-oxide (TMAO) reductases.
Length = 185
Score = 27.0 bits (60), Expect = 3.9
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 2 VACLSPADNNYDETLSTLRYANRAKNIANKP--HINEDPKDTMLREYQ 47
++C DN Y E T+ Y+NR+ A P H+ + D M R+ Q
Sbjct: 49 ISCHEMRDNVYPEYRETIHYSNRSGVRATCPDCHVPHEWTDKMARKVQ 96
>gnl|CDD|240020 cd04662, Nudix_Hydrolase_5, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent
cation, such as Mg2+ or Mn2+, for their activity and
contain a highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. Substrates of
nudix hydrolases include intact and oxidatively damaged
nucleoside triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the
nucleotide pools and to maintain cell viability,
thereby serving as surveillance & "house-cleaning"
enzymes. Substrate specificity is used to define
families within the superfamily. Differences in
substrate specificity are determined by the N-terminal
extension or by residues in variable loop regions.
Mechanistically, substrate hydrolysis occurs by a
nucleophilic substitution reaction, with variation in
the numbers and roles of divalent cations required.
Length = 126
Score = 26.7 bits (59), Expect = 4.2
Identities = 7/19 (36%), Positives = 8/19 (42%)
Query: 32 PHINEDPKDTMLREYQEEI 50
EDP RE+ EE
Sbjct: 42 YTEGEDPLLAAKREFSEET 60
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 27.1 bits (61), Expect = 4.2
Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 4/40 (10%)
Query: 85 EKEKLRLEYEAEMEKLREQYNAERNSKSKMEADLQ-ALKE 123
E EKL+ E E + EKL+E+ E + E + Q A+KE
Sbjct: 545 EAEKLKEELEEKKEKLQEE---EDKLLEEAEKEAQQAIKE 581
>gnl|CDD|236558 PRK09545, znuA, high-affinity zinc transporter periplasmic
component; Reviewed.
Length = 311
Score = 26.9 bits (60), Expect = 4.6
Identities = 12/37 (32%), Positives = 21/37 (56%), Gaps = 3/37 (8%)
Query: 98 EKLREQYNAERNSKSKMEADLQALKEQYQRDMENIGN 134
+KL E SK+K++A+L+ + Q + + IGN
Sbjct: 163 DKLVELMPQ---SKAKLDANLKDFEAQLAQTDKQIGN 196
>gnl|CDD|239519 cd03427, MTH1, MutT homolog-1 (MTH1) is a member of the Nudix
hydrolase superfamily. MTH1, the mammalian counterpart
of MutT, hydrolyzes oxidized purine nucleoside
triphosphates, such as 8-oxo-dGTP and 2-hydroxy-ATP, to
monophosphates, thereby preventing the incorporation of
such oxygen radicals during replication. This is an
important step in the repair mechanism in genomic and
mitochondrial DNA. Like other members of the Nudix
family, it requires a divalent cation, such as Mg2+ or
Mn2+, for activity, and contain the Nudix motif, a
highly conserved 23-residue block (GX5EX7REUXEEXGU,
where U = I, L or V), that functions as a metal binding
and catalytic site. MTH1 is predominantly localized in
the cytoplasm and mitochondria. Structurally, this
enzyme adopts a similar fold to MutT despite low
sequence similarity outside the conserved nudix motif.
The most distinctive structural difference between MutT
and MTH1 is the presence of a beta-hairpin, which is
absent in MutT. This results in a much deeper and
narrower substrate binding pocket. Mechanistically,
MTH1 contains dual specificity for nucleotides that
contain 2-OH-adenine bases and those that contain
8-oxo-guanine bases.
Length = 137
Score = 26.4 bits (59), Expect = 4.7
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 35 NEDPKDTMLREYQEE 49
E P++ +RE +EE
Sbjct: 38 GETPEECAIRELKEE 52
>gnl|CDD|224849 COG1938, COG1938, Archaeal enzymes of ATP-grasp superfamily
[General function prediction only].
Length = 244
Score = 26.9 bits (60), Expect = 4.7
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 3/37 (8%)
Query: 80 STTPLEKEKLRLEYEAEMEKLREQYNAE-RNSKSKME 115
T LEKE E E ++EKL EQ E + + E
Sbjct: 205 DTDKLEKEAE--EIEEQLEKLAEQLEKEEERVEREEE 239
>gnl|CDD|225381 COG2825, HlpA, Outer membrane protein [Cell envelope biogenesis,
outer membrane].
Length = 170
Score = 26.6 bits (59), Expect = 4.8
Identities = 9/41 (21%), Positives = 19/41 (46%), Gaps = 3/41 (7%)
Query: 88 KLRLEYEAEMEKLREQYNAERNSKSKMEADLQALKEQYQRD 128
+ A++E ++ E KM+ +L+A + + Q D
Sbjct: 40 PQAKKVSADLESEFKKRQKE---LQKMQKELKAKEAKLQDD 77
>gnl|CDD|204414 pfam10211, Ax_dynein_light, Axonemal dynein light chain. Axonemal
dynein light chain proteins play a dynamic role in
flagellar and cilia motility. Eukaryotic cilia and
flagella are complex organelles consisting of a core
structure, the axoneme, which is composed of nine
microtubule doublets forming a cylinder that surrounds a
pair of central singlet microtubules. This
ultra-structural arrangement seems to be one of the most
stable micro-tubular assemblies known and is responsible
for the flagellar and ciliary movement of a large number
of organisms ranging from protozoan to mammals. This
light chain interacts directly with the N-terminal half
of the heavy chains.
Length = 189
Score = 26.4 bits (59), Expect = 5.1
Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 6/50 (12%)
Query: 84 LEKEKLRLE-----YEAEMEKLREQYNAERNSKSKMEAD-LQALKEQYQR 127
LE+EK LE EA++E + ++ ER + K AD + LK+Q Q+
Sbjct: 132 LEEEKEELEKRVAELEAKLEAIEKREEEERQIEEKRHADEIAFLKKQNQQ 181
>gnl|CDD|221381 pfam12018, DUF3508, Domain of unknown function (DUF3508). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is about 280
amino acids in length. This domain has two conserved
sequence motifs: GFC and GLL. This family is also known
as UPF0704.
Length = 281
Score = 26.6 bits (59), Expect = 5.6
Identities = 16/84 (19%), Positives = 33/84 (39%), Gaps = 15/84 (17%)
Query: 20 RYANRAKNIANKPHINEDPKDTMLREYQEEIRQLRALLESSGSVPLSGGVCMMNSSSAMD 79
RY + + P + ++ +L+E +RQ A L S ++ + +
Sbjct: 27 RYTAALEEMDENPLMAKELPPYLLKEALYNLRQYEAFLLILLS-------DIILCAQEV- 78
Query: 80 STTPLEKEKLRLEYEAEMEKLREQ 103
E + EA+ME+L++
Sbjct: 79 -------EMNQKRLEAQMEQLKDT 95
>gnl|CDD|192111 pfam08647, BRE1, BRE1 E3 ubiquitin ligase. BRE1 is an E3 ubiquitin
ligase that has been shown to act as a transcriptional
activator through direct activator interactions.
Length = 96
Score = 25.7 bits (57), Expect = 5.8
Identities = 14/49 (28%), Positives = 23/49 (46%)
Query: 86 KEKLRLEYEAEMEKLREQYNAERNSKSKMEADLQALKEQYQRDMENIGN 134
E+ +L AE K ++Y A SK ++A+ + L Q + E I
Sbjct: 29 LEQKKLRLTAEKAKADQKYFAAMRSKDALDAENKKLNTQLNKSSELIEQ 77
>gnl|CDD|135173 PRK04654, PRK04654, sec-independent translocase; Provisional.
Length = 214
Score = 26.7 bits (58), Expect = 5.9
Identities = 14/47 (29%), Positives = 26/47 (55%)
Query: 84 LEKEKLRLEYEAEMEKLREQYNAERNSKSKMEADLQALKEQYQRDME 130
LE E+L+ + LRE + RN++ ++E +AL + RD++
Sbjct: 54 LEAEELKRSLQDVQASLREAEDQLRNTQQQVEQGARALHDDVSRDID 100
>gnl|CDD|216249 pfam01025, GrpE, GrpE.
Length = 165
Score = 26.4 bits (59), Expect = 5.9
Identities = 10/48 (20%), Positives = 24/48 (50%)
Query: 85 EKEKLRLEYEAEMEKLREQYNAERNSKSKMEADLQALKEQYQRDMENI 132
E E E E+E+L E+ ++ ++ A+ + +++ +R+ E
Sbjct: 8 ELEDEEEALEEELEELEEEIEELKDRLLRLLAEFENYRKRTEREREEA 55
>gnl|CDD|145854 pfam02918, Pertussis_S2S3, Pertussis toxin, subunit 2 and 3,
C-terminal domain.
Length = 109
Score = 26.0 bits (57), Expect = 6.0
Identities = 11/38 (28%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 3 ACLSPADNNYDETLSTLR---YANRAKNIANKPHINED 37
AC+SP Y E +TLR Y + + + H++++
Sbjct: 44 ACISPYAGRYREMYATLRRALYTIYRQGLPVRVHVSKE 81
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 26.6 bits (60), Expect = 6.4
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 6/39 (15%)
Query: 79 DSTTPLEKEKLRLEYEAEMEKLREQYN------AERNSK 111
D P EK+++ E E E+ ++ +QY ER +K
Sbjct: 621 DIVIPPEKKEIIEEAEKEVAEIEKQYRRGLITDGERYNK 659
>gnl|CDD|223649 COG0576, GrpE, Molecular chaperone GrpE (heat shock protein)
[Posttranslational modification, protein turnover,
chaperones].
Length = 193
Score = 26.1 bits (58), Expect = 6.5
Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 7/69 (10%)
Query: 71 MMNSSSAMDSTTPLEKEKLRL----EYEAEMEKLREQYNAERNSKSKMEADLQALKEQYQ 126
M + + E E+ E E E + + E+ +++EA L+ LK++Y
Sbjct: 1 MSDKEQKTEEPDAEETEEAEKSEEEEAEEEEPEEENELEEEQQEIAELEAQLEELKDKYL 60
Query: 127 R---DMENI 132
R + EN+
Sbjct: 61 RAQAEFENL 69
>gnl|CDD|233840 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit,
predominant form. Bacteria have a single DNA-directed
RNA polymerase, with required subunits that include
alpha, beta, and beta-prime. This model describes the
predominant architecture of the beta-prime subunit in
most bacteria. This model excludes from among the
bacterial mostly sequences from the cyanobacteria, where
RpoC is replaced by two tandem genes homologous to it
but also encoding an additional domain [Transcription,
DNA-dependent RNA polymerase].
Length = 1140
Score = 26.6 bits (59), Expect = 6.7
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 74 SSSAMDSTTPLEKEKLRLEYEAEMEKLREQYN 105
+ SA D P EK ++ E + E+ K+++ YN
Sbjct: 607 TISASDIVVPDEKYEILKEADKEVAKIQKFYN 638
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 26.6 bits (59), Expect = 6.8
Identities = 11/48 (22%), Positives = 27/48 (56%)
Query: 85 EKEKLRLEYEAEMEKLREQYNAERNSKSKMEADLQALKEQYQRDMENI 132
E E+ E + +E+L E+ + + +K++ +++ L+E+ Q E +
Sbjct: 748 ELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQEEL 795
>gnl|CDD|234173 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members
of this protein family are the bacterial ATP-dependent
chaperone ClpB. This protein belongs to the AAA family,
ATPases associated with various cellular activities
(pfam00004). This molecular chaperone does not act as a
protease, but rather serves to disaggregate misfolded
and aggregated proteins [Protein fate, Protein folding
and stabilization].
Length = 852
Score = 26.5 bits (59), Expect = 8.4
Identities = 13/43 (30%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 84 LEKEKLRLEYEAEMEKLREQYNAERNSKSKMEADLQALKEQYQ 126
L++ ++LE E E K +E+ A + +E +L L+E+Y
Sbjct: 410 LDRRIIQLEIEREALK-KEKDEASKERLEDLEKELAELEEEYA 451
>gnl|CDD|223783 COG0711, AtpF, F0F1-type ATP synthase, subunit b [Energy production
and conversion].
Length = 161
Score = 25.7 bits (57), Expect = 8.6
Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 12/60 (20%)
Query: 85 EKEKLRLEYEAEMEKLREQYNAERNS------------KSKMEADLQALKEQYQRDMENI 132
E + L EYE E+E+ REQ + K++ E +L+ +KE + ++E
Sbjct: 55 EAQALLAEYEQELEEAREQASEIIEQAKKEAEQIAEEIKAEAEEELERIKEAAEAEIEAE 114
>gnl|CDD|217835 pfam03999, MAP65_ASE1, Microtubule associated protein (MAP65/ASE1
family).
Length = 619
Score = 26.4 bits (58), Expect = 8.6
Identities = 25/116 (21%), Positives = 40/116 (34%), Gaps = 14/116 (12%)
Query: 39 KDTMLREYQEEIRQLRALLESSGSVPLSGGVCMMNSSSAMDSTTPLEKEKLRLEYEAEME 98
K E +E + QL L G PLS + A + L L E+E
Sbjct: 100 KAERRAEIKELLHQLLQLCNELGEPPLS-----LLRKDA---------DPLSLPNLEELE 145
Query: 99 KLREQYNAERNSKSKMEADLQALKEQYQRDMENIGNNNSINTGSTDILSTDPDKEF 154
RE+ R K + ++ +LK+ + +G + D+LS
Sbjct: 146 HFRERLGELREEKVRRLEEVDSLKQSIKSLCSLLGTPPARTDFEQDVLSYGEIPND 201
>gnl|CDD|205940 pfam13767, DUF4168, Domain of unknown function (DUF4168).
Length = 78
Score = 24.8 bits (55), Expect = 8.7
Identities = 9/37 (24%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 96 EMEKLREQYNAERNSKSKMEADLQALKEQYQRDMENI 132
+E +R++Y + ++ A+ QAL+++ Q +M
Sbjct: 15 AIEPIRQEY-YQEIQAAEDPAEAQALQQEAQTEMVEA 50
>gnl|CDD|234366 TIGR03825, FliH_bacil, flagellar assembly protein FliH. This
bacillus clade of FliH proteins is not found by the Pfam
FliH model pfam02108, but is closely related to the
sequences identified by that model. Sequences identified
by this model are observed in flagellar operons in an
analogous position relative to other flagellar operon
genes.
Length = 255
Score = 25.9 bits (57), Expect = 9.3
Identities = 11/44 (25%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 85 EKEKLRLEYEAEMEKLREQYNAERNS--KSKMEADLQALKEQYQ 126
E ++ + EA+ +REQ ER + + +A +E Y+
Sbjct: 52 EAAQIIEQAEAQAAAIREQIEQERAQWEEERERLIQEAKQEGYE 95
>gnl|CDD|240033 cd04677, Nudix_Hydrolase_18, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent
cation, such as Mg2+ or Mn2+, for their activity and
contain a highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. Substrates of
nudix hydrolases include intact and oxidatively damaged
nucleoside triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the
nucleotide pools and to maintain cell viability,
thereby serving as surveillance & "house-cleaning"
enzymes. Substrate specificity is used to define
families within the superfamily. Differences in
substrate specificity are determined by the N-terminal
extension or by residues in variable loop regions.
Mechanistically, substrate hydrolysis occurs by a
nucleophilic substitution reaction, with variation in
the numbers and roles of divalent cations required.
Length = 132
Score = 25.6 bits (57), Expect = 9.4
Identities = 6/16 (37%), Positives = 10/16 (62%)
Query: 34 INEDPKDTMLREYQEE 49
+ E ++T RE +EE
Sbjct: 41 LGESLEETARRELKEE 56
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
0.306 0.122 0.324
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,745,594
Number of extensions: 685164
Number of successful extensions: 1227
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1196
Number of HSP's successfully gapped: 246
Length of query: 157
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 68
Effective length of database: 6,990,096
Effective search space: 475326528
Effective search space used: 475326528
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (22.0 bits)
S2: 55 (24.9 bits)