RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15017
(97 letters)
>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 = 148 bits (377), Expect = 1e-45
Identities = 55/87 (63%), Positives = 66/87 (75%)
Query: 3 KIRPQSAREVIDMCRVCTFVTPGEPQVTLGADKSFTFDYVFDMADVQTTIYELCAASLVA 62
++RP +E+++ C+VC V PGEPQVT+G DKSFTFDYVFD + Q +Y C A LV
Sbjct: 8 RVRPLLPKELLEGCQVCVSVVPGEPQVTVGTDKSFTFDYVFDPSTSQEEVYNTCVAPLVD 67
Query: 63 GSLEGYNATILAYGQTGSGKTYTMGTG 89
G EGYNAT+LAYGQTGSGKTYTMGT
Sbjct: 68 GLFEGYNATVLAYGQTGSGKTYTMGTA 94
>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 = 108 bits (271), Expect = 7e-30
Identities = 39/93 (41%), Positives = 46/93 (49%), Gaps = 7/93 (7%)
Query: 2 CKIRPQSAREVIDMCRVCTFVTPGEPQVT-------LGADKSFTFDYVFDMADVQTTIYE 54
++RP + RE + +K FTFD VFD Q ++E
Sbjct: 6 VRVRPLNKREKSRKSPSVVPFPDKVGKTLTVRSPKNRQGEKKFTFDKVFDATASQEDVFE 65
Query: 55 LCAASLVAGSLEGYNATILAYGQTGSGKTYTMG 87
AA LV LEGYNATI AYGQTGSGKTYTM
Sbjct: 66 ETAAPLVDSVLEGYNATIFAYGQTGSGKTYTMI 98
>gnl|CDD|215803 pfam00225, Kinesin, Kinesin motor domain.
Length = 326
Score = 103 bits (260), Expect = 2e-28
Identities = 40/94 (42%), Positives = 47/94 (50%), Gaps = 7/94 (7%)
Query: 4 IRPQSAREVIDMCRVCTFVTPGEPQVTL-------GADKSFTFDYVFDMADVQTTIYELC 56
+RP + RE V + + G +K+FTFD VFD Q +YE
Sbjct: 2 VRPLNEREKSRGSSDIVNVDETDSEDKESVVITNKGREKTFTFDRVFDPEATQEFVYEET 61
Query: 57 AASLVAGSLEGYNATILAYGQTGSGKTYTMGTGT 90
A LV LEGYN TI AYGQTGSGKTYTM
Sbjct: 62 AKPLVESVLEGYNVTIFAYGQTGSGKTYTMEGDP 95
>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 = 97.4 bits (243), Expect = 6e-26
Identities = 37/89 (41%), Positives = 49/89 (55%), Gaps = 4/89 (4%)
Query: 1 MCKIRPQSAREVIDMCRVCTFVTPGEPQVTLGAD---KSFTFDYVFDMADVQTTIYELCA 57
+C+ RP + +E + + PGE V++ K+F+FD VF Q +Y A
Sbjct: 7 VCRFRPLNEKEELRGSKSIVKF-PGEDTVSIAGSDDGKTFSFDRVFPPNTTQEDVYNFVA 65
Query: 58 ASLVAGSLEGYNATILAYGQTGSGKTYTM 86
+V L GYN TI AYGQTGSGKTYTM
Sbjct: 66 KPIVDDVLNGYNGTIFAYGQTGSGKTYTM 94
>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 = 92.7 bits (231), Expect = 3e-24
Identities = 45/93 (48%), Positives = 51/93 (54%), Gaps = 6/93 (6%)
Query: 1 MCKIRPQSAREVIDMCRVCTF-----VTPGEPQVTLGA-DKSFTFDYVFDMADVQTTIYE 54
+ +IRP + RE T VT P+ A KSFTFD+VFD Q +YE
Sbjct: 5 VVRIRPLNGRESKSEESCITVDDNKTVTLTPPKDGRKAGPKSFTFDHVFDPNSTQEDVYE 64
Query: 55 LCAASLVAGSLEGYNATILAYGQTGSGKTYTMG 87
A LV LEGYN TI AYGQTGSGKTYTM
Sbjct: 65 TTAKPLVESVLEGYNGTIFAYGQTGSGKTYTMF 97
>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 = 92.5 bits (230), Expect = 5e-24
Identities = 38/95 (40%), Positives = 47/95 (49%), Gaps = 8/95 (8%)
Query: 1 MCKIRPQSAREVIDMCRVCTFVTPGEPQVTL--------GADKSFTFDYVFDMADVQTTI 52
+ + RP + RE + V QVT+ K FTFD V+D Q +
Sbjct: 6 VVRCRPLNKREKSEGAPEIVGVDENRGQVTVHNPKADAKEPPKVFTFDAVYDPNSTQEDV 65
Query: 53 YELCAASLVAGSLEGYNATILAYGQTGSGKTYTMG 87
Y A LV LEGYN TI AYGQTG+GKT+TM
Sbjct: 66 YNETARPLVDSVLEGYNGTIFAYGQTGTGKTFTME 100
>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 = 83.5 bits (207), Expect = 8e-21
Identities = 29/52 (55%), Positives = 34/52 (65%)
Query: 35 KSFTFDYVFDMADVQTTIYELCAASLVAGSLEGYNATILAYGQTGSGKTYTM 86
+SFTFD VF +YE A +V +LEGYN TI AYGQT SGKT+TM
Sbjct: 40 QSFTFDRVFGGESTNREVYERIAKPVVRSALEGYNGTIFAYGQTSSGKTFTM 91
>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 = 83.1 bits (206), Expect = 1e-20
Identities = 29/57 (50%), Positives = 36/57 (63%), Gaps = 1/57 (1%)
Query: 34 DKSFTFDYVFDMADVQTTIYELCAASLVAGSLEGYNATILAYGQTGSGKTYTMGTGT 90
+ ++FD VFD Q +YE LV G L GYNAT+ AYG TG+GKT+TM GT
Sbjct: 53 ELKYSFDRVFDETSTQEEVYENTTKPLVDGVLNGYNATVFAYGATGAGKTHTM-LGT 108
>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 = 81.8 bits (203), Expect = 4e-20
Identities = 40/91 (43%), Positives = 51/91 (56%), Gaps = 9/91 (9%)
Query: 2 CKIRPQSAREVIDMCRVCTFVTPGEPQVTL------GADKSFTFDYVFDMADVQTTIYEL 55
C++RP E + V +F P E T+ G KSF+FD VFD Q ++E
Sbjct: 8 CRVRPLLPSESTEYSSVISF--PDEDGGTIELSKGTGKKKSFSFDRVFDPDASQEDVFEE 65
Query: 56 CAASLVAGSLEGYNATILAYGQTGSGKTYTM 86
+ LV +L+GYN I AYGQTGSGKTYTM
Sbjct: 66 -VSPLVQSALDGYNVCIFAYGQTGSGKTYTM 95
>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 = 79.7 bits (197), Expect = 3e-19
Identities = 34/99 (34%), Positives = 50/99 (50%), Gaps = 15/99 (15%)
Query: 3 KIRPQSARE-------VIDM-CRVCTFVTPGEPQVTLGADKSFTFDYVFDMAD------- 47
++RP ++RE ++ M +V T P T KSF+FD+ + D
Sbjct: 8 RVRPFNSREKNRGSKCIVQMPGKVTTLKNPKAADATRKKPKSFSFDHSYWSHDSEDPHYA 67
Query: 48 VQTTIYELCAASLVAGSLEGYNATILAYGQTGSGKTYTM 86
Q ++E L+ + EGYN + AYGQTGSGK+YTM
Sbjct: 68 SQEDVFEDLGRELLDHAFEGYNVCLFAYGQTGSGKSYTM 106
>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 = 79.6 bits (197), Expect = 3e-19
Identities = 32/91 (35%), Positives = 49/91 (53%), Gaps = 7/91 (7%)
Query: 3 KIRPQSAREVIDMCRVCTFVTPGEPQVTL-------GADKSFTFDYVFDMADVQTTIYEL 55
+ RP+++RE + V V+ ++ + + K++TFD VF Q +Y
Sbjct: 9 RCRPRNSRERKEKSSVVVEVSGSSKEIIVSTGGADKQSTKTYTFDKVFGPEADQIEVYSQ 68
Query: 56 CAASLVAGSLEGYNATILAYGQTGSGKTYTM 86
+ ++ L GYN TI AYGQTG+GKTYTM
Sbjct: 69 VVSPILDEVLMGYNCTIFAYGQTGTGKTYTM 99
>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 = 74.1 bits (182), Expect = 3e-17
Identities = 33/85 (38%), Positives = 42/85 (49%), Gaps = 1/85 (1%)
Query: 3 KIRPQSAREVIDMCRVCTFVTPGEPQVTLG-ADKSFTFDYVFDMADVQTTIYELCAASLV 61
+IRP + E C + V + FTFD+V D Q +++ LV
Sbjct: 8 RIRPPNEIEADGGQGQCLKKLSSDTLVWHSHPPRMFTFDHVADSNTNQEDVFQSVGKPLV 67
Query: 62 AGSLEGYNATILAYGQTGSGKTYTM 86
L GYN +I AYGQTGSGKTYTM
Sbjct: 68 EDCLSGYNGSIFAYGQTGSGKTYTM 92
>gnl|CDD|227392 COG5059, KIP1, Kinesin-like protein [Cytoskeleton].
Length = 568
Score = 73.2 bits (180), Expect = 9e-17
Identities = 32/98 (32%), Positives = 45/98 (45%), Gaps = 16/98 (16%)
Query: 2 CKIRPQSAREVIDMCRVCTFVTPGEP--QVTLGADKS-----------FTFDYVFDMADV 48
R + + + + + PGE ++ + KS + FD VF +
Sbjct: 13 LSSRNE---KSVSDIKSTIRIIPGELGERLINTSKKSHVSLEKSKEGTYAFDKVFGPSAT 69
Query: 49 QTTIYELCAASLVAGSLEGYNATILAYGQTGSGKTYTM 86
Q +YE L+ L GYN T+ AYGQTGSGKTYTM
Sbjct: 70 QEDVYEETIKPLIDSLLLGYNCTVFAYGQTGSGKTYTM 107
>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 = 71.7 bits (176), Expect = 2e-16
Identities = 32/61 (52%), Positives = 40/61 (65%), Gaps = 3/61 (4%)
Query: 34 DKSFTFDYVFDMADVQTTIYELCAASLVAGSLEGYNATILAYGQTGSGKTYTM--GTGTF 91
D SF FD VF A Q +YE A +V +L+GYN TI AYGQTG+GKT+TM GT ++
Sbjct: 47 DFSFKFDGVFHNAS-QEEVYETVAKPVVDSALDGYNGTIFAYGQTGAGKTFTMTGGTESY 105
Query: 92 S 92
Sbjct: 106 K 106
>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 = 69.6 bits (171), Expect = 1e-15
Identities = 27/52 (51%), Positives = 30/52 (57%)
Query: 36 SFTFDYVFDMADVQTTIYELCAASLVAGSLEGYNATILAYGQTGSGKTYTMG 87
+F FDYVFD A +Y L+ EG AT AYGQTGSGKTYTM
Sbjct: 52 TFRFDYVFDEAVTNEEVYRSTVKPLIPHVFEGGVATCFAYGQTGSGKTYTML 103
>gnl|CDD|215621 PLN03188, PLN03188, kinesin-12 family protein; Provisional.
Length = 1320
Score = 68.4 bits (167), Expect = 5e-15
Identities = 27/52 (51%), Positives = 36/52 (69%)
Query: 35 KSFTFDYVFDMADVQTTIYELCAASLVAGSLEGYNATILAYGQTGSGKTYTM 86
++FTFD + D Q I++L A LV L G+N+++ AYGQTGSGKTYTM
Sbjct: 132 QTFTFDSIADPESTQEDIFQLVGAPLVENCLAGFNSSVFAYGQTGSGKTYTM 183
>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 = 60.1 bits (146), Expect = 3e-12
Identities = 30/104 (28%), Positives = 43/104 (41%), Gaps = 16/104 (15%)
Query: 2 CKIRPQSAREVIDMCRVC------TFVTPGEPQVTLG---------ADKSFTFDYVFDMA 46
++RP S E+ C T + P+ + + F+F VF
Sbjct: 7 LRVRPLSKDELESEDEGCIEVINSTTIQLHPPKGSAARKSERNGGQKETKFSFSKVFGPN 66
Query: 47 DVQTTIYELCAASLVAGSLEGYNATILAYGQTGSGKTYTMGTGT 90
Q +E A LV L+G N+ + YG T SGKTYTM G+
Sbjct: 67 TTQKEFFEGTALPLVQDLLKGKNSLLFTYGVTNSGKTYTM-QGS 109
>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 = 56.3 bits (136), Expect = 7e-11
Identities = 22/55 (40%), Positives = 29/55 (52%)
Query: 32 GADKSFTFDYVFDMADVQTTIYELCAASLVAGSLEGYNATILAYGQTGSGKTYTM 86
G K + FD + Q I+ +V L G NAT+ AYG TG+GKT+TM
Sbjct: 44 GETKKYQFDAFYGTECTQEDIFSREVKPIVPHLLSGQNATVFAYGSTGAGKTHTM 98
>gnl|CDD|238659 cd01363, Motor_domain, Myosin and Kinesin motor domain. These
ATPases belong to the P-loop NTPase family and provide
the driving force in myosin and kinesin mediated
processes.
Length = 186
Score = 51.8 bits (124), Expect = 1e-09
Identities = 19/35 (54%), Positives = 24/35 (68%), Gaps = 1/35 (2%)
Query: 52 IYELCAASLVAGSLEGYNATILAYGQTGSGKTYTM 86
++ L+ +L+GYN I AYGQTGSGKTYTM
Sbjct: 8 VFRDVG-PLLQSALDGYNVCIFAYGQTGSGKTYTM 41
>gnl|CDD|235395 PRK05298, PRK05298, excinuclease ABC subunit B; Provisional.
Length = 652
Score = 33.5 bits (78), Expect = 0.008
Identities = 14/29 (48%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 58 ASLVAGSLEGYNATILAYGQTGSGKTYTM 86
LV G G L G TGSGKT+TM
Sbjct: 22 EELVEGIEAGEKHQTL-LGVTGSGKTFTM 49
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair
complex [DNA replication, recombination, and repair].
Length = 663
Score = 31.4 bits (72), Expect = 0.050
Identities = 15/29 (51%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 58 ASLVAGSLEGYNATILAYGQTGSGKTYTM 86
A LV G G L G TGSGKT+TM
Sbjct: 22 AELVEGIENGLKHQTL-LGVTGSGKTFTM 49
>gnl|CDD|216796 pfam01935, DUF87, Domain of unknown function DUF87. The function
of this prokaryotic domain is unknown. It contains
several conserved aspartates and histidines that could
be metal ligands.
Length = 218
Score = 29.6 bits (67), Expect = 0.17
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 75 YGQTGSGKTYTMGT 88
G TGSGK+ T+
Sbjct: 29 LGSTGSGKSNTVAV 42
>gnl|CDD|223587 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA
replication, recombination, and repair / Transcription
/ Translation, ribosomal structure and biogenesis].
Length = 513
Score = 29.4 bits (66), Expect = 0.21
Identities = 10/32 (31%), Positives = 14/32 (43%), Gaps = 2/32 (6%)
Query: 65 LEGYNATILAYGQTGSGKTYTMGTGTFSPISR 96
L G + +L QTG+GKT I +
Sbjct: 64 LAGRD--VLGQAQTGTGKTAAFLLPLLQKILK 93
>gnl|CDD|233063 TIGR00631, uvrb, excinuclease ABC, B subunit. All proteins in
this family for wich functions are known are DNA
helicases that function in the nucleotide excision
repair and are endonucleases that make the 3' incision
next to DNA damage. They are part of a pathway
requiring UvrA, UvrB, UvrC, and UvrD homologs. This
family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and
repair].
Length = 655
Score = 29.2 bits (66), Expect = 0.29
Identities = 15/29 (51%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 58 ASLVAGSLEGYNATILAYGQTGSGKTYTM 86
A LV G +G L G TGSGKT+TM
Sbjct: 19 AKLVEGLTDGEKHQTL-LGVTGSGKTFTM 46
>gnl|CDD|221803 pfam12846, AAA_10, AAA-like domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily. Many of the proteins in this family
are conjugative transfer proteins.
Length = 316
Score = 27.8 bits (62), Expect = 0.85
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 69 NATILAYGQTGSGKTYTMGT 88
N +L G +GSGK+ +
Sbjct: 1 NPNMLIVGPSGSGKSTLLKL 20
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 27.7 bits (62), Expect = 0.86
Identities = 12/27 (44%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 57 AASLVAGSLEGYNATILAYGQTGSGKT 83
A + SL G+ +L G TGSGKT
Sbjct: 206 AVEAILSSLGGFAPFLL-DGVTGSGKT 231
>gnl|CDD|234063 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation
protein. Members of this protein family are found
exclusively in the archaea. This set of DNA binding
proteins shows homology to the origin recognition
complex subunit 1/cell division control protein 6
family in eukaryotes. Several members may be found in
genome and interact with each other [DNA metabolism,
DNA replication, recombination, and repair].
Length = 365
Score = 27.6 bits (62), Expect = 0.87
Identities = 7/12 (58%), Positives = 10/12 (83%)
Query: 72 ILAYGQTGSGKT 83
+ YG+TG+GKT
Sbjct: 43 VFIYGKTGTGKT 54
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 27.6 bits (62), Expect = 0.95
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 69 NATILAYGQTGSGKTY 84
N +L YG TG+GKT+
Sbjct: 183 NENLLFYGNTGTGKTF 198
>gnl|CDD|148296 pfam06603, UpxZ, UpxZ family of transcription anti-terminator
antagonists. The UpxZ family of proteins acts to
inhibit transcription of heterologous capsular
polysaccharide loci in Bacteroides species by
interfering with the action of the UpxY family of
transcription anti-terminators. As antagonists of
polysaccharide locus-specific UpxY transcription
anti-terminators, the UpxZ proteins exert a
hierarchical level of regulation, insuring that only
one of the multiple phase-variable capsular
polysaccharide loci per cell characteristic of this
genus is transcribed at a time.
Length = 106
Score = 26.5 bits (59), Expect = 1.2
Identities = 14/49 (28%), Positives = 19/49 (38%), Gaps = 13/49 (26%)
Query: 41 YVFDMADVQTTIYELCA-------------ASLVAGSLEGYNATILAYG 76
Y D++ + + EL A+L L GYNATI G
Sbjct: 23 YSDDLSRLNKEVLELSNDLYSQKGETPEEEANLCLALLMGYNATIYNNG 71
>gnl|CDD|236694 PRK10436, PRK10436, hypothetical protein; Provisional.
Length = 462
Score = 27.2 bits (61), Expect = 1.4
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 72 ILAYGQTGSGKTYTM 86
IL G TGSGKT T+
Sbjct: 221 ILVTGPTGSGKTVTL 235
>gnl|CDD|226350 COG3829, RocR, Transcriptional regulator containing PAS, AAA-type
ATPase, and DNA-binding domains [Transcription / Signal
transduction mechanisms].
Length = 560
Score = 27.3 bits (61), Expect = 1.4
Identities = 8/25 (32%), Positives = 16/25 (64%), Gaps = 4/25 (16%)
Query: 58 ASLVAGSLEGYNATILAYGQTGSGK 82
A +A + ++T+L G++G+GK
Sbjct: 261 AKRIAKT----DSTVLILGESGTGK 281
>gnl|CDD|233406 TIGR01420, pilT_fam, pilus retraction protein PilT. This model
represents the PilT subfamily of proteins related to
GspE, a protein involved in type II secretion (also
called the General Secretion Pathway). PilT is an
apparent cytosolic ATPase associated with type IV pilus
systems. It is not required for pilin biogenesis, but is
required for twitching motility and social gliding
behaviors, shown in some species, powered by pilus
retraction. Members of this family may be found in some
species that type IV pili but have related structures
for DNA uptake and natural transformation [Cell
envelope, Surface structures, Cellular processes,
Chemotaxis and motility].
Length = 343
Score = 27.3 bits (61), Expect = 1.4
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 72 ILAYGQTGSGKTYTM 86
IL G TGSGK+ T+
Sbjct: 125 ILVTGPTGSGKSTTL 139
>gnl|CDD|225364 COG2805, PilT, Tfp pilus assembly protein, pilus retraction ATPase
PilT [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 353
Score = 27.2 bits (61), Expect = 1.4
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 72 ILAYGQTGSGKTYTM 86
IL G TGSGK+ T+
Sbjct: 128 ILVTGPTGSGKSTTL 142
>gnl|CDD|222290 pfam13654, AAA_32, AAA domain. This family includes a wide
variety of AAA domains including some that have lost
essential nucleotide binding residues in the P-loop.
Length = 509
Score = 27.0 bits (61), Expect = 1.6
Identities = 8/21 (38%), Positives = 12/21 (57%), Gaps = 2/21 (9%)
Query: 66 EGYNATILAYGQTGSGKTYTM 86
GYN I G+ G+G+T +
Sbjct: 29 PGYN--IFVLGEPGTGRTTLV 47
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 26.7 bits (59), Expect = 1.6
Identities = 11/22 (50%), Positives = 11/22 (50%), Gaps = 1/22 (4%)
Query: 65 LEGYNATILAYGQTGSGKTYTM 86
L G ILA TGSGKT
Sbjct: 21 LSGLRDVILA-APTGSGKTLAA 41
>gnl|CDD|223683 COG0610, COG0610, Type I site-specific restriction-modification
system, R (restriction) subunit and related helicases
[Defense mechanisms].
Length = 962
Score = 27.0 bits (60), Expect = 1.6
Identities = 7/9 (77%), Positives = 7/9 (77%)
Query: 78 TGSGKTYTM 86
GSGKT TM
Sbjct: 282 QGSGKTLTM 290
>gnl|CDD|226132 COG3604, FhlA, Transcriptional regulator containing GAF, AAA-type
ATPase, and DNA binding domains [Transcription / Signal
transduction mechanisms].
Length = 550
Score = 26.9 bits (60), Expect = 1.6
Identities = 11/32 (34%), Positives = 19/32 (59%), Gaps = 5/32 (15%)
Query: 52 IYELC-AASLVAGSLEGYNATILAYGQTGSGK 82
+ +L +VA S ++T+L G+TG+GK
Sbjct: 232 MRQLLKEIEVVAKS----DSTVLIRGETGTGK 259
>gnl|CDD|215758 pfam00158, Sigma54_activat, Sigma-54 interaction domain.
Length = 168
Score = 26.6 bits (60), Expect = 1.7
Identities = 7/17 (41%), Positives = 12/17 (70%)
Query: 68 YNATILAYGQTGSGKTY 84
+AT+L G++G+GK
Sbjct: 21 TDATVLITGESGTGKEL 37
>gnl|CDD|223403 COG0326, HtpG, Molecular chaperone, HSP90 family [Posttranslational
modification, protein turnover, chaperones].
Length = 623
Score = 26.8 bits (60), Expect = 1.9
Identities = 19/63 (30%), Positives = 28/63 (44%), Gaps = 11/63 (17%)
Query: 12 VIDMCRVCTFVTPGEPQVTLGADKSFTFDYVFDMADVQTTIYELCAASLVA--GS--LEG 67
++D+ R + GE V+L +YV M + Q IY + S A GS LE
Sbjct: 393 LLDLLRFRSTSDSGEKTVSLE-------EYVSRMKEGQKQIYYITGESYQAAKGSPHLEL 445
Query: 68 YNA 70
+ A
Sbjct: 446 FKA 448
>gnl|CDD|216952 pfam02264, LamB, LamB porin. Maltoporin (LamB protein) forms a
trimeric structure which facilitates the diffusion of
maltodextrins across the outer membrane of Gram-negative
bacteria. The membrane channel is formed by an
antiparallel beta-barrel.
Length = 399
Score = 26.7 bits (59), Expect = 2.0
Identities = 10/39 (25%), Positives = 16/39 (41%)
Query: 58 ASLVAGSLEGYNATILAYGQTGSGKTYTMGTGTFSPISR 96
A L G L G+N + YG G+ + G + +
Sbjct: 210 AELTQGLLNGFNKFVFQYGTAGTALNFGHFWGAGTKYNG 248
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 26.0 bits (58), Expect = 2.0
Identities = 7/9 (77%), Positives = 7/9 (77%)
Query: 78 TGSGKTYTM 86
TGSGKT T
Sbjct: 27 TGSGKTLTA 35
>gnl|CDD|233914 TIGR02538, type_IV_pilB, type IV-A pilus assembly ATPase PilB.
This model describes a protein of type IV pilus
biogenesis designated PilB in Pseudomonas aeruginosa but
PilF in Neisseria gonorrhoeae; the more common usage,
reflected here, is PilB. This protein is an ATPase
involved in protein export for pilin assembly and is
closely related to GspE (TIGR02533) of type II
secretion, also called the main terminal branch of the
general secretion pathway. Note that type IV pilus
systems are often divided into type IV-A and IV-B, with
the latter group including bundle-forming pilus,
mannose-sensitive hemagglutinin, etc. Members of this
family are found in type IV-A systems [Cell envelope,
Surface structures, Protein fate, Protein and peptide
secretion and trafficking].
Length = 564
Score = 26.5 bits (59), Expect = 2.2
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 72 ILAYGQTGSGKTYTMGTG 89
+L G TGSGKT ++ T
Sbjct: 319 VLVTGPTGSGKTVSLYTA 336
>gnl|CDD|193522 cd05644, M28_like_3, M28 Zn-Peptidases. Peptidase family M28 (also
called aminopeptidase Y family), uncharacterized
subfamily. The M28 family contains aminopeptidases as
well as carboxypeptidases. They typically have
co-catalytic zinc ions; each zinc ion is tetrahedrally
co-ordinated, with three amino acid ligands plus
activated water; one aspartate residue binds both metal
ions. Proteins in this subfamily conserve some of the
metal-coordinating residues of the typically
co-catalytic M28 family, and appear to bind a single
metal (Zn) ion.
Length = 415
Score = 26.4 bits (59), Expect = 2.3
Identities = 16/49 (32%), Positives = 21/49 (42%), Gaps = 8/49 (16%)
Query: 7 QSAREVIDMCRVCTFVTPGEPQV-------TLGADKSFTFDYVFDMADV 48
+ EV++ RV P EPQ+ TL KS + D V M V
Sbjct: 331 REVIEVLENNRVYKNTVPCEPQLGKRGLYPTLSG-KSDSGDQVMAMLWV 378
>gnl|CDD|225363 COG2804, PulE, Type II secretory pathway, ATPase PulE/Tfp pilus
assembly pathway, ATPase PilB [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 500
Score = 26.5 bits (59), Expect = 2.3
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 72 ILAYGQTGSGKTYTM 86
IL G TGSGKT T+
Sbjct: 261 ILVTGPTGSGKTTTL 275
>gnl|CDD|238549 cd01129, PulE-GspE, PulE/GspE The type II secretory pathway is the
main terminal branch of the general secretory pathway
(GSP). It is responsible for the export the majority of
Gram-negative bacterial exoenzymes and toxins. PulE is a
cytoplasmic protein of the GSP, which contains an ATP
binding site and a tetracysteine motif. This subgroup
also includes PillB and HofB.
Length = 264
Score = 26.1 bits (58), Expect = 2.6
Identities = 12/26 (46%), Positives = 16/26 (61%), Gaps = 4/26 (15%)
Query: 72 ILAYGQTGSGKTYTMGTGTFSPISRI 97
IL G TGSGKT T+ +S +S +
Sbjct: 83 ILVTGPTGSGKTTTL----YSALSEL 104
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 26.3 bits (59), Expect = 2.7
Identities = 9/13 (69%), Positives = 9/13 (69%)
Query: 72 ILAYGQTGSGKTY 84
IL G TGSGKT
Sbjct: 111 ILLIGPTGSGKTL 123
>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 26.1 bits (58), Expect = 2.9
Identities = 11/30 (36%), Positives = 15/30 (50%)
Query: 57 AASLVAGSLEGYNATILAYGQTGSGKTYTM 86
AA VA + G + YG G GKT+ +
Sbjct: 101 AAKAVAENPGGAYNPLFIYGGVGLGKTHLL 130
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 26.2 bits (58), Expect = 2.9
Identities = 11/30 (36%), Positives = 14/30 (46%), Gaps = 2/30 (6%)
Query: 55 LCAASLVAGSLEGYNATILAYGQTGSGKTY 84
ASLV G N ++ G G GKT+
Sbjct: 93 EDLASLVEFFERGEN--LVLLGPPGVGKTH 120
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 26.3 bits (59), Expect = 3.1
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 10/51 (19%)
Query: 44 DMADVQTTIYELCAASLVAGSLEGYNATILAYGQTGSGKTYTMGTGTFSPI 94
+M +Q A SL A L G + ++A +TGSGKT G G +
Sbjct: 26 EMTPIQ-------AQSLPA-ILAGKD--VIAQAKTGSGKTAAFGLGLLQKL 66
>gnl|CDD|227355 COG5022, COG5022, Myosin heavy chain [Cytoskeleton].
Length = 1463
Score = 26.2 bits (58), Expect = 3.3
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 66 EGYNATILAYGQTGSGKT 83
E N TI+ G++G+GKT
Sbjct: 149 EKENQTIIISGESGAGKT 166
>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 169
Score = 25.7 bits (57), Expect = 3.4
Identities = 7/12 (58%), Positives = 8/12 (66%)
Query: 72 ILAYGQTGSGKT 83
+L TGSGKT
Sbjct: 17 VLVQAPTGSGKT 28
>gnl|CDD|219014 pfam06414, Zeta_toxin, Zeta toxin. This family consists of
several bacterial zeta toxin proteins. Zeta toxin is
thought to be part of a postregulational killing system
in bacteria. It relies on antitoxin/toxin systems that
secure stable inheritance of low and medium copy number
plasmids during cell division and kill cells that have
lost the plasmid.
Length = 191
Score = 25.7 bits (57), Expect = 3.5
Identities = 8/16 (50%), Positives = 10/16 (62%), Gaps = 1/16 (6%)
Query: 70 ATILAYGQTGSGKTYT 85
A +L GQ G+GKT
Sbjct: 14 AVLLG-GQPGAGKTEL 28
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 26.1 bits (58), Expect = 3.6
Identities = 10/19 (52%), Positives = 11/19 (57%), Gaps = 2/19 (10%)
Query: 65 LEGYNATILAYGQTGSGKT 83
G N I+A TGSGKT
Sbjct: 35 HSGENVLIIA--PTGSGKT 51
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only
detects a fraction of this vast family. The poorly
conserved N-terminal helix is missing from the
alignment.
Length = 148
Score = 25.4 bits (55), Expect = 4.2
Identities = 8/16 (50%), Positives = 8/16 (50%)
Query: 71 TILAYGQTGSGKTYTM 86
IL G GSGKT
Sbjct: 4 VILIVGPPGSGKTTLA 19
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 25.9 bits (58), Expect = 4.4
Identities = 9/20 (45%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 64 SLEGYNATILAYGQTGSGKT 83
+ G++ +L G TGSGKT
Sbjct: 158 AAAGFSPFLL-DGVTGSGKT 176
>gnl|CDD|238550 cd01130, VirB11-like_ATPase, Type IV secretory pathway component
VirB11, and related ATPases. The homohexamer, VirB11 is
one of eleven Vir proteins, which are required for
T-pilus biogenesis and virulence in the transfer of
T-DNA from the Ti (tumor-inducing) plasmid of bacterial
to plant cells. The pilus is a fibrous cell surface
organelle, which mediates adhesion between bacteria
during conjugative transfer or between bacteria and
host eukaryotic cells during infection. VirB11- related
ATPases include the archaeal flagella biosynthesis
protein and the pilus assembly proteins CpaF/TadA and
TrbB. This alignment contains the C-terminal domain,
which is the ATPase.
Length = 186
Score = 25.7 bits (57), Expect = 4.4
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 71 TILAYGQTGSGKTYTM 86
IL G TGSGKT +
Sbjct: 27 NILISGGTGSGKTTLL 42
>gnl|CDD|227347 COG5014, COG5014, Predicted Fe-S oxidoreductase [General function
prediction only].
Length = 228
Score = 25.6 bits (56), Expect = 4.4
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 5/36 (13%)
Query: 4 IRPQSAREVIDMCRVCTFV--TPGEPQVTLGADKSF 37
+ + EVI++ TFV T G + G D+S
Sbjct: 104 LGREHVLEVIELLVNNTFVLETNG---LMFGFDRSL 136
>gnl|CDD|238680 cd01384, MYSc_type_XI, Myosin motor domain, plant-specific type XI
myosin, involved in organelle transport. This catalytic
(head) domain has ATPase activity and belongs to the
larger group of P-loop NTPases. Myosins are
actin-dependent molecular motors that play important
roles in muscle contraction, cell motility, and
organelle transport. The head domain is a molecular
motor, which utilizes ATP hydrolysis to generate
directed movement toward the plus end along actin
filaments. A cyclical interaction between myosin and
actin provides the driving force. Rates of ATP
hydrolysis and consequently the speed of movement along
actin filaments vary widely, from about 0.04 micrometer
per second for myosin I to 4.5 micrometer per second for
myosin II in skeletal muscle. Myosin II moves in
discrete steps about 5-10 nm long and generates 1-5
piconewtons of force. Upon ATP binding, the myosin head
dissociates from an actin filament. ATP hydrolysis
causes the head to pivot and associate with a new actin
subunit. The release of Pi causes the head to pivot and
move the filament (power stroke). Release of ADP
completes the cycle.
Length = 674
Score = 25.8 bits (57), Expect = 5.0
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 66 EGYNATILAYGQTGSGKTYT 85
EG + +IL G++G+GKT T
Sbjct: 85 EGKSQSILVSGESGAGKTET 104
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 25.4 bits (56), Expect = 5.0
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 72 ILAYGQTGSGKTYTM 86
I+ YG TG+GKT T+
Sbjct: 45 IIIYGPTGTGKTATV 59
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase
fold. The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons,
ATPase subunits of proteases, helicases, or
nucleic-acid stimulated ATPases. The AAA+ proteins
contain several distinct features in addition to the
conserved alpha-beta-alpha core domain structure and
the Walker A and B motifs of the P-loop NTPases.
Length = 151
Score = 25.2 bits (55), Expect = 5.1
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 72 ILAYGQTGSGKTYTM 86
+L YG G+GKT
Sbjct: 22 LLLYGPPGTGKTTLA 36
>gnl|CDD|238551 cd01131, PilT, Pilus retraction ATPase PilT. PilT is a nucleotide
binding protein responsible for the retraction of type
IV pili, likely by pili disassembly. This retraction
provides the force required for travel of bacteria in
low water environments by a mechanism known as
twitching motility.
Length = 198
Score = 25.0 bits (55), Expect = 6.3
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 72 ILAYGQTGSGKTYTM 86
+L G TGSGK+ T+
Sbjct: 4 VLVTGPTGSGKSTTL 18
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 25.0 bits (55), Expect = 6.4
Identities = 8/16 (50%), Positives = 9/16 (56%), Gaps = 1/16 (6%)
Query: 71 TILAYGQTGSGKTYTM 86
+LA TGSGKT
Sbjct: 3 VLLA-APTGSGKTLAA 17
>gnl|CDD|172375 PRK13851, PRK13851, type IV secretion system protein VirB11;
Provisional.
Length = 344
Score = 25.2 bits (55), Expect = 6.4
Identities = 16/41 (39%), Positives = 18/41 (43%), Gaps = 8/41 (19%)
Query: 63 GSLEGYNA-------TILAYGQTGSGKTYTMGTGTFSPISR 96
G LE + T+L G TGSGKT TM S I
Sbjct: 149 GDLEAFLHACVVGRLTMLLCGPTGSGKT-TMSKTLISAIPP 188
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 25.2 bits (56), Expect = 6.5
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 72 ILAYGQTGSGKTYTM 86
+L YG G+GKT T+
Sbjct: 58 VLIYGPPGTGKTTTV 72
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 24.9 bits (55), Expect = 6.5
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 72 ILAYGQTGSGKTYTM 86
+ G++GSGKT +
Sbjct: 7 GVLTGESGSGKTTLL 21
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 25.3 bits (56), Expect = 6.6
Identities = 9/13 (69%), Positives = 9/13 (69%)
Query: 72 ILAYGQTGSGKTY 84
IL G TGSGKT
Sbjct: 100 ILLIGPTGSGKTL 112
>gnl|CDD|223703 COG0630, VirB11, Type IV secretory pathway, VirB11 components, and
related ATPases involved in archaeal flagella
biosynthesis [Cell motility and secretion /
Intracellular trafficking and secretion].
Length = 312
Score = 25.0 bits (55), Expect = 6.6
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 51 TIYELCAASLVAGSLEGYNATILAYGQTGSGKTYTM 86
TI AA L ++E +I+ G T SGKT +
Sbjct: 127 TISPEQAAYLWL-AIE-ARKSIIICGGTASGKTTLL 160
>gnl|CDD|238167 cd00268, DEADc, DEAD-box helicases. A diverse family of proteins
involved in ATP-dependent RNA unwinding, needed in a
variety of cellular processes including splicing,
ribosome biogenesis and RNA degradation. The name
derives from the sequence of the Walker B motif (motif
II). This domain contains the ATP- binding region.
Length = 203
Score = 25.1 bits (56), Expect = 6.7
Identities = 9/19 (47%), Positives = 12/19 (63%), Gaps = 2/19 (10%)
Query: 65 LEGYNATILAYGQTGSGKT 83
L G + ++ QTGSGKT
Sbjct: 34 LSGRD--VIGQAQTGSGKT 50
>gnl|CDD|234340 TIGR03744, traC_PFL_4706, conjugative transfer ATPase, PFL_4706
family. Members of this protein family are predicted
ATP-binding proteins apparently associated with DNA
conjugal transfer. Members are found both in plasmids
and in bacterial chromosomal regions that appear to
derive from integrative elements such as conjugative
transposons. More distant homologs, outside the scope of
this family, include type IV secretion/conjugal transfer
proteins such as TraC, VirB4 and TrsE. The granularity
of this protein family definition is chosen so as to
represent one distinctive clade and act as a marker
through which to define and recognize the class of
mobile element it serves [Mobile and extrachromosomal
element functions, Plasmid functions].
Length = 893
Score = 25.4 bits (56), Expect = 7.0
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 69 NATILAYGQTGSGKTYTM 86
NA +L G TG+GK+ T+
Sbjct: 475 NAHLLILGPTGAGKSATL 492
>gnl|CDD|200328 TIGR03819, heli_sec_ATPase, helicase/secretion neighborhood ATPase.
Members of this protein family comprise a distinct
clade of putative ATPase associated with an integral
membrane complex likely to act in pilus formation,
secretion, or conjugal transfer. The association of most
members with a nearby gene for a DEAH-box helicase
suggests a role in conjugal transfer.
Length = 340
Score = 25.0 bits (55), Expect = 8.0
Identities = 16/56 (28%), Positives = 22/56 (39%), Gaps = 9/56 (16%)
Query: 51 TIYELCAASLVAGSLEGYNATILA-------YGQTGSGKTYTMGT--GTFSPISRI 97
T+ EL AA + + ++A G TGSGKT + P RI
Sbjct: 153 TLDELVAAGTIPPGVARLLRALVAARLAFLVSGGTGSGKTTLLSALLALVPPDERI 208
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a
wide variety of presumed phage proteins.
Length = 201
Score = 24.9 bits (55), Expect = 8.4
Identities = 9/20 (45%), Positives = 10/20 (50%)
Query: 69 NATILAYGQTGSGKTYTMGT 88
N +L YG G GKT T
Sbjct: 3 NIKVLIYGPPGIGKTSLAKT 22
>gnl|CDD|238957 cd01999, Argininosuccinate_Synthase, Argininosuccinate synthase.
The Argininosuccinate synthase is a urea cycle enzyme
that catalyzes the penultimate step in arginine
biosynthesis: the ATP-dependent ligation of citrulline
to aspartate to form argininosuccinate, AMP and
pyrophosphate . In humans, a defect in the AS gene
causes citrullinemia, a genetic disease characterized by
severe vomiting spells and mental retardation. AS is a
homotetrameric enzyme of chains of about 400 amino-acid
residues. An arginine seems to be important for the
enzyme's catalytic mechanism. The sequences of AS from
various prokaryotes, archaebacteria and eukaryotes show
significant similarity.
Length = 385
Score = 24.8 bits (55), Expect = 8.5
Identities = 19/66 (28%), Positives = 28/66 (42%), Gaps = 16/66 (24%)
Query: 29 VTLGADKSFTFDYVFDMADVQT-TIYE------------LCAASLVAGSLEGYNATILAY 75
V + + F DY+F +Q +YE L A +LV + E A +A+
Sbjct: 56 VVVDLREEFVEDYIFPA--IQANALYEGTYPLGTALARPLIAKALVEVAKE-EGADAVAH 112
Query: 76 GQTGSG 81
G TG G
Sbjct: 113 GCTGKG 118
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
0.322 0.135 0.403
Gapped
Lambda K H
0.267 0.0643 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,735,955
Number of extensions: 372333
Number of successful extensions: 569
Number of sequences better than 10.0: 1
Number of HSP's gapped: 563
Number of HSP's successfully gapped: 78
Length of query: 97
Length of database: 10,937,602
Length adjustment: 64
Effective length of query: 33
Effective length of database: 8,098,946
Effective search space: 267265218
Effective search space used: 267265218
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.4 bits)