RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15463
(68 letters)
>gnl|CDD|238673 cd01377, MYSc_type_II, Myosin motor domain, type II myosins.
Myosin II mediates cortical contraction in cell
motility, and is the motor in smooth and skeletal
muscle. 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 = 693
Score = 119 bits (300), Expect = 2e-33
Identities = 40/54 (74%), Positives = 48/54 (88%)
Query: 5 TYSGLFCVVVNPYKRLPIYTEKIMERYKGVKRLDVPPHVFAITDNAYRSMLQGK 58
TYSGLFCV VNPYKRLPIYTE+++E Y+G KR ++PPH+FAI DNAYRSMLQ +
Sbjct: 36 TYSGLFCVAVNPYKRLPIYTEEVVEMYRGKKREEMPPHIFAIADNAYRSMLQDR 89
>gnl|CDD|214580 smart00242, MYSc, Myosin. Large ATPases. ATPase; molecular
motor. Muscle contraction consists of a cyclical
interaction between myosin and actin. The core of the
myosin structure is similar in fold to that of kinesin.
Length = 677
Score = 101 bits (255), Expect = 3e-27
Identities = 33/54 (61%), Positives = 44/54 (81%)
Query: 5 TYSGLFCVVVNPYKRLPIYTEKIMERYKGVKRLDVPPHVFAITDNAYRSMLQGK 58
TY GL V VNPYK+LPIYT++++++Y+G R ++PPHVFAI DNAYR+ML K
Sbjct: 37 TYIGLVLVAVNPYKQLPIYTDEVIKKYRGKSRGELPPHVFAIADNAYRNMLNDK 90
>gnl|CDD|215687 pfam00063, Myosin_head, Myosin head (motor domain).
Length = 679
Score = 93.1 bits (232), Expect = 3e-24
Identities = 31/52 (59%), Positives = 41/52 (78%)
Query: 5 TYSGLFCVVVNPYKRLPIYTEKIMERYKGVKRLDVPPHVFAITDNAYRSMLQ 56
TYSGL + VNPYKRLPIYTE+ + Y+G +R ++PPH+FA+ D AYR ML+
Sbjct: 30 TYSGLVLISVNPYKRLPIYTEEPIGEYRGKRRGELPPHIFALADRAYRHMLR 81
>gnl|CDD|238674 cd01378, MYSc_type_I, Myosin motor domain, type I myosins. Myosin
I generates movement at the leading edge in cell
motility, and class I myosins have been implicated in
phagocytosis and vesicle transport. Myosin I, an
unconventional myosin, does not form dimers. 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 = 90.0 bits (224), Expect = 4e-23
Identities = 28/52 (53%), Positives = 39/52 (75%)
Query: 5 TYSGLFCVVVNPYKRLPIYTEKIMERYKGVKRLDVPPHVFAITDNAYRSMLQ 56
TY G + VNP+K+LPIYT++ +E YKG R ++PPH++A+ DNAYRSM
Sbjct: 31 TYIGPVLISVNPFKQLPIYTDETIELYKGKSRYELPPHIYALADNAYRSMKS 82
>gnl|CDD|227355 COG5022, COG5022, Myosin heavy chain [Cytoskeleton].
Length = 1463
Score = 87.8 bits (218), Expect = 2e-22
Identities = 28/52 (53%), Positives = 38/52 (73%)
Query: 5 TYSGLFCVVVNPYKRLPIYTEKIMERYKGVKRLDVPPHVFAITDNAYRSMLQ 56
TYSGL + VNPY+ L IYT+ I++ Y G RL++ PHVFAI + AYR++L
Sbjct: 97 TYSGLVLIAVNPYRDLGIYTDDIIQSYSGKNRLELEPHVFAIAEEAYRNLLS 148
>gnl|CDD|238071 cd00124, MYSc, Myosin motor domain. 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 = 679
Score = 84.6 bits (210), Expect = 3e-21
Identities = 27/52 (51%), Positives = 37/52 (71%)
Query: 5 TYSGLFCVVVNPYKRLPIYTEKIMERYKGVKRLDVPPHVFAITDNAYRSMLQ 56
TY+G + VNPYK LP Y + + +Y+G R ++PPHVFAI D AYR+ML+
Sbjct: 31 TYAGPILIAVNPYKDLPNYGPETIRKYRGKSRSELPPHVFAIADRAYRNMLR 82
>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 = 71.2 bits (175), Expect = 1e-16
Identities = 26/52 (50%), Positives = 37/52 (71%), Gaps = 1/52 (1%)
Query: 5 TYSGLFCVVVNPYKRLP-IYTEKIMERYKGVKRLDVPPHVFAITDNAYRSML 55
TY+G + VNP++RLP +Y +ME+YKG ++ PHVFAI D AYR+M+
Sbjct: 32 TYTGNILIAVNPFQRLPHLYDVHMMEQYKGAALGELSPHVFAIADAAYRAMI 83
>gnl|CDD|238677 cd01381, MYSc_type_VII, Myosin motor domain, type VII myosins.
Myosins in this group have been associated with
functions in sensory systems such as vision and
hearing. 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 = 671
Score = 67.5 bits (165), Expect = 3e-15
Identities = 26/50 (52%), Positives = 35/50 (70%)
Query: 5 TYSGLFCVVVNPYKRLPIYTEKIMERYKGVKRLDVPPHVFAITDNAYRSM 54
TY+G V VNPY+ LPIYT ++ YK ++PPH+FAI+DNAY +M
Sbjct: 31 TYTGSILVAVNPYQILPIYTADEIKLYKNKSIGELPPHIFAISDNAYTNM 80
>gnl|CDD|238676 cd01380, MYSc_type_V, Myosin motor domain, type V myosins.
Myosins V transport a variety of intracellular cargo
processively along actin filaments, such as membraneous
organelles and mRNA. 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 = 691
Score = 65.0 bits (159), Expect = 2e-14
Identities = 25/55 (45%), Positives = 39/55 (70%)
Query: 4 KTYSGLFCVVVNPYKRLPIYTEKIMERYKGVKRLDVPPHVFAITDNAYRSMLQGK 58
TYSG+ V +NPY RLPIY E+I++ Y G ++ ++ PH+FAI + AY+ M + +
Sbjct: 30 YTYSGIVLVAINPYARLPIYGEEIIQAYSGQRKGELDPHIFAIAEEAYKQMTRDE 84
>gnl|CDD|238681 cd01385, MYSc_type_IX, Myosin motor domain, type IX myosins.
Myosin IX is a processive single-headed motor, which
might play a role in signalling. 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 = 692
Score = 60.3 bits (146), Expect = 1e-12
Identities = 28/55 (50%), Positives = 37/55 (67%), Gaps = 1/55 (1%)
Query: 5 TYSGLFCVVVNPYKRLPIYTEKIMERYKGVKRL-DVPPHVFAITDNAYRSMLQGK 58
TY+G V VNP+K LPIY K + Y+ +RL +PPH+FAI D AY +ML+ K
Sbjct: 38 TYAGSILVAVNPFKFLPIYNPKYVRLYENQQRLGKLPPHIFAIADVAYYNMLRKK 92
>gnl|CDD|238675 cd01379, MYSc_type_III, Myosin motor domain, type III myosins.
Myosin III has been shown to play a role in the vision
process in insects and in hearing in mammals. Myosin
III, an unconventional myosin, does not form dimers.
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 = 653
Score = 59.5 bits (144), Expect = 2e-12
Identities = 23/51 (45%), Positives = 33/51 (64%)
Query: 5 TYSGLFCVVVNPYKRLPIYTEKIMERYKGVKRLDVPPHVFAITDNAYRSML 55
TY G + VNP+++L +YT + Y G KR PPH+FAI D AY+S++
Sbjct: 31 TYVGDILIAVNPFQQLGLYTTQHSRLYTGQKRSSNPPHIFAIADAAYQSLV 81
>gnl|CDD|238682 cd01386, MYSc_type_XVIII, Myosin motor domain, type XVIII
myosins. 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 = 767
Score = 57.2 bits (138), Expect = 2e-11
Identities = 19/52 (36%), Positives = 35/52 (67%)
Query: 5 TYSGLFCVVVNPYKRLPIYTEKIMERYKGVKRLDVPPHVFAITDNAYRSMLQ 56
T +G +V+NP L +Y+EK+ ++G K D+PPH++++ AYR++L+
Sbjct: 31 TCAGPDLLVLNPMAPLALYSEKVPSMFRGCKAEDMPPHIYSLAQTAYRALLE 82
>gnl|CDD|238678 cd01382, MYSc_type_VI, Myosin motor domain, type VI myosins.
Myosin VI is a monomeric myosin, which moves towards
the minus-end of actin filaments, in contrast to most
other myosins. It has been implicated in endocytosis,
secretion, and cell migration. 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
minus 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 = 717
Score = 52.1 bits (125), Expect = 9e-10
Identities = 22/51 (43%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 5 TYSGLFCVVVNPYKRLP-IYTEKIMERYKGVKRLDVPPHVFAITDNAYRSM 54
TY + VNPY +P +Y+ +++Y+G +PPHVFAI D AYR M
Sbjct: 35 TYVANILIAVNPYFDIPKLYSSDTIKKYQGKSLGTLPPHVFAIADKAYRDM 85
>gnl|CDD|238683 cd01387, MYSc_type_XV, Myosin motor domain, type XV myosins. In
vertebrates, myosin XV appears to be expressed in
sensory tissue and play a role in hearing. 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 = 677
Score = 50.7 bits (121), Expect = 3e-09
Identities = 24/55 (43%), Positives = 32/55 (58%)
Query: 5 TYSGLFCVVVNPYKRLPIYTEKIMERYKGVKRLDVPPHVFAITDNAYRSMLQGKT 59
TY G V VNPYK PIY + +++Y G + PPH+FAI + A+ ML K
Sbjct: 32 TYIGSILVSVNPYKMFPIYGPEQVQQYAGRALGENPPHLFAIANLAFAKMLDAKQ 86
>gnl|CDD|238679 cd01383, MYSc_type_VIII, Myosin motor domain, plant-specific type
VIII myosins, a subgroup which has been associated with
endocytosis, cytokinesis, cell-to-cell coupling and
gating at plasmodesmata. 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 = 677
Score = 48.7 bits (116), Expect = 1e-08
Identities = 21/52 (40%), Positives = 32/52 (61%), Gaps = 2/52 (3%)
Query: 5 TYSGLFCVVVNPYKRLPIYTEKIMERYKGVKRLDVPPHVFAITDNAYRSMLQ 56
T +G V VNP+K +P+Y +E Y+ K+ + PHV+AI D AY M++
Sbjct: 39 TKAGPVLVAVNPFKEVPLYGNDYIEAYR--KKSNDSPHVYAIADTAYNEMMR 88
>gnl|CDD|240229 PTZ00014, PTZ00014, myosin-A; Provisional.
Length = 821
Score = 34.6 bits (80), Expect = 0.001
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 12 VVVNPYKRLPIYTEKIMERYKGVKRLD-VPPHVFAITDNA 50
V +NP+K L T + RY+ K D +PPHVF A
Sbjct: 134 VAINPFKDLGNTTNDWIRRYRDAKDSDKLPPHVFTTARRA 173
>gnl|CDD|226485 COG3977, COG3977, Alanine-alpha-ketoisovalerate (or
valine-pyruvate) aminotransferase [Amino acid transport
and metabolism].
Length = 417
Score = 26.7 bits (59), Expect = 0.86
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 17 YKRLPIYTEKIMERYKGVKRLDVPPHVFAI 46
+K LPI TE++ +R K L VP H F
Sbjct: 345 FKDLPITTEELYQRLKARGVLMVPGHYFFP 374
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 26.2 bits (58), Expect = 1.3
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 41 PHVFAITDNAYRSM 54
PHV +T+ +YRSM
Sbjct: 310 PHVAGVTEYSYRSM 323
>gnl|CDD|215513 PLN02951, PLN02951, Molybderin biosynthesis protein CNX2.
Length = 373
Score = 25.5 bits (56), Expect = 2.6
Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 3/28 (10%)
Query: 18 KRLPIYTE---KIMERYKGVKRLDVPPH 42
K+L Y E +I +R+ +KRL P
Sbjct: 247 KKLVPYAEMMDRIEQRFPSLKRLQDHPT 274
>gnl|CDD|238935 cd01976, Nitrogenase_MoFe_alpha, Nitrogenase_MoFe_alpha_II:
Nitrogenase MoFe protein, beta subunit. A group of
proteins similar to the alpha subunit of the MoFe
protein of the molybdenum (Mo-) nitrogenase. The
nitrogenase enzyme catalyzes the ATP-dependent reduction
of dinitrogen to ammonia. The Mo-nitrogenase is the most
widespread and best characterized of these systems.
Mo-nitrogenase consists of the MoFe protein (component
1) and the Fe protein (component 2). MoFe is an
alpha2beta2 tetramer. Each alphabeta pair of MoFe
contains one P-cluster (at the alphabeta interface) and,
one molecule of iron molybdenum cofactor (FeMoco)
contained within the alpha subunit. The Fe protein
contains a single [4Fe-4S] cluster. Electrons are
transferred from the [4Fe-4S] cluster of the Fe protein
to the P-cluster of the MoFe and in turn to FeMoCo, the
site of substrate reduction.
Length = 421
Score = 25.0 bits (55), Expect = 2.9
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 12/45 (26%)
Query: 24 TEKIMERYKGVKRLDVPPHVFAITDNAYRSMLQGKTALTRELWVG 68
TE+++ YK P + A+ YR L+GKT + L+VG
Sbjct: 276 TEEVIAEYK--------PAMEAVIA-KYRPRLEGKTVM---LYVG 308
>gnl|CDD|233397 TIGR01405, polC_Gram_pos, DNA polymerase III, alpha chain,
Gram-positive type. This model describes a polypeptide
chain of DNA polymerase III. Full-length homologs of
this protein are restricted to the Gram-positive
lineages, including the Mycoplasmas. This protein is
designated alpha chain and given the gene symbol polC,
but is not a full-length homolog of other polC genes.
The N-terminal region of about 200 amino acids is rich
in low-complexity sequence, poorly alignable, and not
included n this model [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1213
Score = 25.0 bits (55), Expect = 2.9
Identities = 8/29 (27%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 14 VNPYKRLPIYTEKIMERYKGVKRLDVPPH 42
++P K +P+ +++M + K L V P
Sbjct: 884 IDP-KTIPMDDKEVMSIFSSPKALGVTPE 911
>gnl|CDD|162284 TIGR01282, nifD, nitrogenase molybdenum-iron protein alpha chain.
Nitrogenase consists of alpha (NifD) and beta (NifK)
subunits of the molybdenum-iron protein and an
ATP-binding iron-sulfur protein (NifH). This model
describes a large clade of NifD proteins, but excludes a
lineage that contains putative NifD and NifD homologs
from species with vanadium-dependent nitrogenases
[Central intermediary metabolism, Nitrogen fixation].
Length = 466
Score = 24.6 bits (54), Expect = 4.1
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 12/45 (26%)
Query: 24 TEKIMERYKGVKRLDVPPHVFAITDNAYRSMLQGKTALTRELWVG 68
E+++ +Y+ P V A+ YR L+GKT + L+VG
Sbjct: 311 AEEVIAKYQ--------PAVDAVIA-KYRPRLEGKTVM---LYVG 343
>gnl|CDD|216958 pfam02278, Lyase_8, Polysaccharide lyase family 8, super-sandwich
domain. This family consists of a group of secreted
bacterial lyase enzymes EC:4.2.2.1 capable of acting on
hyaluronan and chondroitin in the extracellular matrix
of host tissues, contributing to the invasive capacity
of the pathogen.
Length = 269
Score = 24.5 bits (53), Expect = 4.4
Identities = 17/63 (26%), Positives = 22/63 (34%), Gaps = 4/63 (6%)
Query: 6 YSGLFCVVVNPYKRLPIYTEKIMERYKGVKRLDVPPHVF---AITDNAYRSMLQGKTALT 62
YS F V+ YK LP TE+ +R K V D+ Y + T
Sbjct: 68 YSDWFWPTVDWYK-LPGTTERDAKRADPTKEWGVQKSNDFVGGKLDDVYAAAGMDFTNWD 126
Query: 63 REL 65
L
Sbjct: 127 DTL 129
>gnl|CDD|224548 COG1633, COG1633, Uncharacterized conserved protein [Function
unknown].
Length = 176
Score = 23.9 bits (52), Expect = 6.9
Identities = 8/36 (22%), Positives = 12/36 (33%)
Query: 2 TWKTYSGLFCVVVNPYKRLPIYTEKIMERYKGVKRL 37
T + Y L +VN + T E+ L
Sbjct: 128 TIEFYEELLDELVNEEAKKLFKTIADDEKGHASGLL 163
>gnl|CDD|169401 PRK08359, PRK08359, transcription factor; Validated.
Length = 176
Score = 24.1 bits (52), Expect = 7.4
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 16 PYKRLPIYTEKIMERY 31
P + P+YTE I+E Y
Sbjct: 71 PRRERPLYTEDIVEDY 86
>gnl|CDD|179499 PRK02913, PRK02913, hypothetical protein; Provisional.
Length = 150
Score = 23.7 bits (52), Expect = 8.1
Identities = 10/19 (52%), Positives = 11/19 (57%)
Query: 22 IYTEKIMERYKGVKRLDVP 40
IY + IM R KG L VP
Sbjct: 18 IYDQFIMPRRKGKTLLKVP 36
>gnl|CDD|238929 cd01967, Nitrogenase_MoFe_alpha_like, Nitrogenase_MoFe_alpha_like:
Nitrogenase MoFe protein, alpha subunit_like. The
nitrogenase enzyme catalyzes the ATP-dependent reduction
of dinitrogen to ammonia. Three genetically distinct
types of nitrogenase systems are known to exist: a
molybdenum-dependent nitrogenase (Mo-nitrogenase), a
vanadium dependent nitrogenase (V-nitrogenase), and an
iron-only nitrogenase (Fe-nitrogenase). These
nitrogenase systems consist of component 1 (MoFe
protein, VFe protein or, FeFe protein respectively) and,
component 2 (Fe protein). This group contains the alpha
subunit of component 1 of all three different forms. The
most widespread and best characterized of these systems
is the Mo-nitrogenase. MoFe is an alpha2beta2 tetramer,
the alternative nitrogenases are alpha2beta2delta2
hexamers having alpha and beta subunits similar to the
alpha and beta subunits of MoFe. The role of the delta
subunit is unknown. For MoFe, each alphabeta pair of
subunits contains one P-cluster (located at the
alphabeta interface) and, one molecule of iron
molybdenum cofactor (FeMoco) contained within the alpha
subunit. The Fe protein is a homodimer which contains, a
single [4Fe-4S] cluster from which electrons are
transferred to the P-cluster of the MoFe and in turn,
to FeMoCo the site of substrate reduction. The
V-nitrogenase requires an iron-vanadium cofactor
(FeVco), the iron only-nitrogenase an iron only cofactor
(FeFeco). These cofactors are analogous to the FeMoco.
The V-nitrogenase has P clusters identical to those of
MoFe. In addition to N2, nitrogenase also catalyzes the
reduction of a variety of other substrates such as
acetylene The V-nitrogenase differs from the Mo-
nitrogenase in that it produces free hydrazine, as a
minor product during dinitrogen reduction and, ethane
as a minor product during acetylene reduction.
Length = 406
Score = 23.7 bits (52), Expect = 8.7
Identities = 8/47 (17%), Positives = 17/47 (36%), Gaps = 16/47 (34%)
Query: 24 TEKIMERYKGV--KRLDVPPHVFAITDNAYRSMLQGKTALTRELWVG 68
E+++ + L+ YR L+GK + ++ G
Sbjct: 262 AEEVIAEEEARIKPELE-----------KYRERLKGKKVI---IYTG 294
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
0.324 0.139 0.443
Gapped
Lambda K H
0.267 0.0809 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,554,463
Number of extensions: 261241
Number of successful extensions: 367
Number of sequences better than 10.0: 1
Number of HSP's gapped: 362
Number of HSP's successfully gapped: 27
Length of query: 68
Length of database: 10,937,602
Length adjustment: 39
Effective length of query: 29
Effective length of database: 9,207,796
Effective search space: 267026084
Effective search space used: 267026084
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.0 bits)