RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12657
(260 letters)
>gnl|CDD|201683 pfam01245, Ribosomal_L19, Ribosomal protein L19.
Length = 113
Score = 64.8 bits (159), Expect = 2e-13
Identities = 33/88 (37%), Positives = 44/88 (50%), Gaps = 3/88 (3%)
Query: 9 DIPSFFVGSILSVTSADKHDPNKTR--KFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAY 66
D+P F VG + V K + NK R F G+ I KR GL F +R + +G+E +
Sbjct: 15 DLPEFRVGDTVKVHVKIK-EGNKERIQVFEGVVIAKRGRGLNSTFTVRKISQGVGVERVF 73
Query: 67 DLYDPTIHNITVLRLEKRLDDDLLYLRD 94
L+ P I I V+R K L YLRD
Sbjct: 74 PLHSPRIDKIEVVRRGKVRRAKLYYLRD 101
>gnl|CDD|223412 COG0335, RplS, Ribosomal protein L19 [Translation, ribosomal
structure and biogenesis].
Length = 115
Score = 50.7 bits (122), Expect = 3e-08
Identities = 29/88 (32%), Positives = 44/88 (50%), Gaps = 3/88 (3%)
Query: 9 DIPSFFVGSILSVTSADKHDPNKTR--KFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAY 66
DIPSF G + V + +K R F G+ I +R G+ F +R + +G+E +
Sbjct: 17 DIPSFRPGDTVRVHVKIV-EGSKERVQAFEGVVIARRGRGISETFTVRKISYGVGVERVF 75
Query: 67 DLYDPTIHNITVLRLEKRLDDDLLYLRD 94
L+ P I +I V+R K L YLR+
Sbjct: 76 PLHSPLIESIEVVRRGKVRRAKLYYLRE 103
>gnl|CDD|130096 TIGR01024, rplS_bact, ribosomal protein L19, bacterial type. This
model describes bacterial ribosomoal protein L19 and its
chloroplast equivalent. Putative mitochondrial L19 are
found in several species (but not Saccharomyces
cerevisiae) and score between trusted and noise cutoffs
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 113
Score = 45.8 bits (109), Expect = 1e-06
Identities = 28/88 (31%), Positives = 43/88 (48%), Gaps = 3/88 (3%)
Query: 9 DIPSFFVGSILSVTSADKHDPNKTR--KFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAY 66
D+P F VG + V + K R F G+ I +R G+ F +R + +G+E +
Sbjct: 15 DLPDFRVGDTVRVHVKIV-EGKKERIQVFEGVVIARRGGGIGETFTVRKISYGVGVERIF 73
Query: 67 DLYDPTIHNITVLRLEKRLDDDLLYLRD 94
L+ P I +I V+R K L YLR+
Sbjct: 74 PLHSPNIDSIEVVRRGKVRRAKLYYLRE 101
>gnl|CDD|235418 PRK05338, rplS, 50S ribosomal protein L19; Provisional.
Length = 116
Score = 40.5 bits (96), Expect = 1e-04
Identities = 26/78 (33%), Positives = 38/78 (48%), Gaps = 11/78 (14%)
Query: 9 DIPSFFVGSILSVTSADKH----DPNKTR--KFVGICIQKRYCGLRHEFVLRNVVDNLGI 62
DIP F G + V H + NK R F G+ I +R GL F +R + +G+
Sbjct: 15 DIPEFRPGDTVRV-----HVKVVEGNKERIQAFEGVVIARRGRGLNETFTVRKISYGVGV 69
Query: 63 EIAYDLYDPTIHNITVLR 80
E + L+ P I +I V+R
Sbjct: 70 ERTFPLHSPRIDSIEVVR 87
>gnl|CDD|177023 CHL00084, rpl19, ribosomal protein L19.
Length = 117
Score = 36.1 bits (84), Expect = 0.004
Identities = 24/91 (26%), Positives = 41/91 (45%), Gaps = 7/91 (7%)
Query: 8 IDIPSFFVGSI----LSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIE 63
++P VG + + +K + + + G I K+ GL +R V +G+E
Sbjct: 18 KNLPKIRVGDTVKVGVLIQEGNK---ERVQFYEGTVIAKKNSGLNTTITVRKVFQGIGVE 74
Query: 64 IAYDLYDPTIHNITVLRLEKRLDDDLLYLRD 94
+ L+ P + +I VLR K L YLR+
Sbjct: 75 RVFLLHSPKLASIEVLRRSKVRRAKLYYLRN 105
>gnl|CDD|234876 PRK00960, PRK00960, seryl-tRNA synthetase; Provisional.
Length = 517
Score = 33.1 bits (76), Expect = 0.13
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 134 YLRDALPQYSTFPFDMEPEY-LLDGAPVPINDIKVKLKPRP-WVGRWERKGYKGIDDVDQ 191
LRD P Y P EP Y G V ++++ +K R W RWE G G++ V++
Sbjct: 304 KLRD--PGYVLAPAQCEPFYQFFQGETVDVDELPIKFFDRSGWTYRWEGGGAHGLERVNE 361
>gnl|CDD|237463 PRK13668, PRK13668, hypothetical protein; Provisional.
Length = 267
Score = 31.1 bits (71), Expect = 0.40
Identities = 23/88 (26%), Positives = 35/88 (39%), Gaps = 20/88 (22%)
Query: 123 RLEKRLDDDLLYLRDALPQYSTFPFDMEPEYLLDGAPVPINDI----KVKLKPRPWVGRW 178
+L+KRL P + F FD E E L I V + P V +W
Sbjct: 9 KLKKRLSH---------PDW-DFSFDREKETLR------IERKDNKKGVTISLPPIVAKW 52
Query: 179 ERKGYKGIDDVDQHITEKMKGQKKKLEE 206
E K K ID++ ++ E + K++
Sbjct: 53 EEKKEKAIDEIVYYVEEALAAMADKVKL 80
>gnl|CDD|216146 pfam00843, Arena_nucleocap, Arenavirus nucleocapsid protein.
Length = 533
Score = 31.2 bits (71), Expect = 0.52
Identities = 21/58 (36%), Positives = 28/58 (48%), Gaps = 8/58 (13%)
Query: 78 VLRLEKRLDDDLLYLRDALPNVVDNLGIEIAYDMYDPTIHNITVLRLEKRLDDDLLYL 135
++R EKR D DL LRD L VDNL M + VL++ D+L+ L
Sbjct: 50 LMRKEKRDDSDLTRLRD-LNKEVDNL-------MSMKSTQKNNVLKVGGLSKDELMEL 99
>gnl|CDD|129509 TIGR00415, serS_MJ, seryl-tRNA synthetase, Methanococcus jannaschii
family. The seryl-tRNA synthetases from a few of the
Archaea, represented by this model, are very different
from the set of mutually more closely related seryl-tRNA
synthetases from Eubacteria, Eukaryotes, and other
Archaea. Although distantly homologous, the present set
differs enough not to be recognized by the pfam model
tRNA-synt_2b that recognizes the remainder of seryl-tRNA
synthetases among oither class II amino-acyl tRNA
synthetases [Protein synthesis, tRNA aminoacylation].
Length = 520
Score = 31.1 bits (70), Expect = 0.62
Identities = 20/59 (33%), Positives = 27/59 (45%), Gaps = 4/59 (6%)
Query: 135 LRDALPQYSTFPFDMEPEY-LLDGAPVPINDIKVKLKPRP-WVGRWERKGYKGIDDVDQ 191
++D P Y P EP Y +G + D +K R W RWE G KG+D V +
Sbjct: 305 IKD--PGYVIAPAQCEPFYQFFEGEVIDAEDKPIKFFDRSGWTYRWEAGGAKGLDRVHE 361
>gnl|CDD|227185 COG4848, COG4848, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 265
Score = 30.6 bits (69), Expect = 0.72
Identities = 24/112 (21%), Positives = 49/112 (43%), Gaps = 9/112 (8%)
Query: 119 ITVLRLEKRLDDDLLYLRDALPQYSTFPFDMEPEYLLDGAPVPINDIKVKLKPRPWVGRW 178
+T ++ +L++ L + TF +D E + L N + + P + ++
Sbjct: 1 MTTRKMRDQLEERLNHPN------RTFSYDREEDTL--RIEDTENKKGITIALPPIIAKY 52
Query: 179 ERKGYKGIDDVDQHITEKMKGQKKKLEEPWEKYDLMKEYRRT-IPEEEQEEI 229
ERKG + ID++ ++ E M K K E + + R T P++ ++
Sbjct: 53 ERKGERAIDEIVYYVQEGMAAMKGKTTEKGNEKRIYPVIRATSFPDKTKDGH 104
>gnl|CDD|216950 pfam02259, FAT, FAT domain. The FAT domain is named after FRAP,
ATM and TRRAP.
Length = 350
Score = 30.8 bits (70), Expect = 0.76
Identities = 8/30 (26%), Positives = 15/30 (50%)
Query: 210 KYDLMKEYRRTIPEEEQEEIFSEVFSELHQ 239
++D M EY ++ E + F + LH+
Sbjct: 13 QWDEMDEYLSSMKEASPDRSFYQALLALHR 42
>gnl|CDD|184468 PRK14035, PRK14035, citrate synthase; Provisional.
Length = 371
Score = 29.7 bits (67), Expect = 1.6
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 12/57 (21%)
Query: 184 KGIDDVDQHITEKMKGQKK---------KLEEPWEKYDLMKEYRRTIPEE-EQEEIF 230
+ I DVD ++ EK ++K K +P KY ++E R I + +EE+F
Sbjct: 233 RSIGDVDAYLDEKFANKEKIMGFGHRVYKDGDPRAKY--LREMSRKITKGTGREELF 287
>gnl|CDD|143386 cd00141, NT_POLXc, Nucleotidyltransferase (NT) domain of family X
DNA Polymerases. X family polymerases fill in short
gaps during DNA repair. They are relatively inaccurate
enzymes and play roles in base excision repair, in
non-homologous end joining (NHEJ) which acts mainly to
repair damage due to ionizing radiation, and in V(D)J
recombination. This family includes eukaryotic Pol beta,
Pol lambda, Pol mu, and terminal deoxyribonucleotidyl
transferase (TdT). Pol beta and Pol lambda are primarily
DNA template-dependent polymerases. TdT is a DNA
template-independent polymerase. Pol mu has both
template dependent and template independent activities.
This subgroup belongs to the Pol beta-like NT
superfamily. In the majority of enzymes in this
superfamily, two carboxylates, Dx[D/E], together with a
third more distal carboxylate, coordinate two divalent
metal cations involved in a two-metal ion mechanism of
nucleotide addition. These three carboxylate residues
are fairly well conserved in this family.
Length = 307
Score = 29.5 bits (67), Expect = 1.8
Identities = 11/67 (16%), Positives = 27/67 (40%), Gaps = 8/67 (11%)
Query: 175 VGRWERKGYKGIDDVDQHITEKM-KGQKKKLEEPWEKYDLMKEYRRTIPEEEQEEIFSEV 233
+ G + ++D+ + K+ + LE +++++ IP EE I +
Sbjct: 98 ARKLYELGIRTLEDLRKAAGAKLEQNILIGLE-------YYEDFQQRIPREEALAIAEII 150
Query: 234 FSELHQL 240
L ++
Sbjct: 151 KEALREV 157
>gnl|CDD|176468 cd01596, Aspartase_like, aspartase (L-aspartate ammonia-lyase) and
fumarase class II enzymes. This group contains
aspartase (L-aspartate ammonia-lyase), fumarase class II
enzymes, and related proteins. It is a member of the
Lyase class I family. Members of this family for the
most part catalyze similar beta-elimination reactions in
which a C-N or C-O bond is cleaved with the release of
fumarate as one of the products. These proteins are
active as tetramers. The four active sites of the
homotetrameric enzyme are each formed by residues from
three different subunits. Aspartase catalyzes the
reversible deamination of aspartic acid. Fumarase
catalyzes the reversible hydration/dehydration of
fumarate to L-malate during the Krebs cycle.
Length = 450
Score = 28.9 bits (66), Expect = 2.5
Identities = 11/26 (42%), Positives = 13/26 (50%)
Query: 71 PTIHNITVLRLEKRLDDDLLYLRDAL 96
P H L L +RL L L+DAL
Sbjct: 141 PAAHIAAALALLERLLPALEQLQDAL 166
Score = 28.9 bits (66), Expect = 2.5
Identities = 11/26 (42%), Positives = 13/26 (50%)
Query: 114 PTIHNITVLRLEKRLDDDLLYLRDAL 139
P H L L +RL L L+DAL
Sbjct: 141 PAAHIAAALALLERLLPALEQLQDAL 166
>gnl|CDD|239871 cd04406, RhoGAP_myosin_IXA, RhoGAP_myosin_IXA: RhoGAP
(GTPase-activator protein [GAP] for Rho-like small
GTPases) domain present in myosins IXA. Class IX myosins
contain a characteristic head domain, a neck domain and
a tail domain which contains a C6H2-zinc binding motif
and a Rho-GAP domain. Class IX myosins are
single-headed, processive myosins that are partly
cytoplasmic, and partly associated with membranes and
the actin cytoskeleton. Class IX myosins are implicated
in the regulation of neuronal morphogenesis and function
of sensory systems, like the inner ear. There are two
major isoforms, myosin IXA and IXB with several splice
variants, which are both expressed in developing
neurons. Small GTPases cluster into distinct families,
and all act as molecular switches, active in their
GTP-bound form but inactive when GDP-bound. The Rho
family of GTPases activates effectors involved in a wide
variety of developmental processes, including regulation
of cytoskeleton formation, cell proliferation and the
JNK signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 186
Score = 28.4 bits (63), Expect = 3.2
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 186 IDDVDQH-ITEKMKGQKKKLEEPWEKYDLMKEYRRTIPEEEQEEIFSEVFSELHQLS 241
+DD + H I K + L P ++L +E+ R + +E+ E V+S + QLS
Sbjct: 62 LDDYNIHVIASVFKQWLRDLPNPLMTFELYEEFLRAMGLQERRETVRGVYSVIDQLS 118
>gnl|CDD|220350 pfam09700, Cas_Cmr3, CRISPR-associated protein (Cas_Cmr3). CRISPR
is a term for Clustered Regularly Interspaced Short
Palindromic Repeats. A number of protein families appear
only in association with these repeats and are
designated Cas (CRISPR associated) proteins. This highly
divergent family, found in at least ten different
archaeal and bacterial species, is represented by TM1793
from Thermotoga maritima.
Length = 347
Score = 28.5 bits (64), Expect = 3.3
Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 8/79 (10%)
Query: 159 PVPINDIKVKLKPR---PWVGRWERKGYKGIDDVDQHITEKMKGQKKKLEEPWEKYDLMK 215
P P+ D+ VK++ + R E G + D D ++ G+K+ L K
Sbjct: 86 PAPL-DLLVKVEKEDGLVNLLRLEPLGPLPLPDRDPLEEPRIGGKKEPAPGYLSLEGLEK 144
Query: 216 EYRRTIPE----EEQEEIF 230
R +PE E+EEIF
Sbjct: 145 WLRGELPEDSELVEEEEIF 163
>gnl|CDD|222347 pfam13729, TraF_2, F plasmid transfer operon, TraF, protein.
Length = 267
Score = 28.4 bits (64), Expect = 3.7
Identities = 22/103 (21%), Positives = 32/103 (31%), Gaps = 10/103 (9%)
Query: 55 NVVDNLG-IEIAYDLYDPTIHNITVLRLEKRLDDDLLYLRDALPNVVDNLGIEIAYDMYD 113
N+VD + YD + N V RL L L G+ +A + +
Sbjct: 34 NLVDKFDDLSDIYDALSSALDNSDVDAAAARLAGALRDLDGDTAYA--QAGVGLAVAIPN 91
Query: 114 PTIH-------NITVLRLEKRLDDDLLYLRDALPQYSTFPFDM 149
+ T + D DL YL D T D+
Sbjct: 92 QPLSMAFFAKAYGTAIVTADVSDSDLDYLDDVDNGTPTDLNDL 134
>gnl|CDD|181439 PRK08472, fliI, flagellum-specific ATP synthase; Validated.
Length = 434
Score = 28.5 bits (64), Expect = 3.9
Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 198 KGQKKKLEEPWEKYDLMKEYRRTIPEEEQEEIFSEVFSELHQL 240
KG K+L+E K + M+++ + P E F + F +L ++
Sbjct: 392 KGNDKELDEAISKKEFMEQFLKQNPNELFP--FEQTFEQLEEI 432
>gnl|CDD|182473 PRK10455, PRK10455, periplasmic protein; Reviewed.
Length = 161
Score = 27.8 bits (62), Expect = 4.1
Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 9/69 (13%)
Query: 156 DGAPVPINDIKVKLKPRPWVGRWERKGYKGIDDVD---QHITEKMKGQKKKLEEPWEKYD 212
D P D K + + G +KG++ D Q I + MK Q+ +++ P
Sbjct: 25 DTTTAPPADAKPMMHHKGKFGPHHDMMFKGLNLTDAQKQQIRDIMKAQRDQMKRP----- 79
Query: 213 LMKEYRRTI 221
E RR +
Sbjct: 80 -PLEERRAM 87
>gnl|CDD|227669 COG5378, COG5378, Predicted nucleotide-binding protein [General
function prediction only].
Length = 175
Score = 27.6 bits (61), Expect = 5.7
Identities = 10/50 (20%), Positives = 25/50 (50%)
Query: 186 IDDVDQHITEKMKGQKKKLEEPWEKYDLMKEYRRTIPEEEQEEIFSEVFS 235
+D++ +HI +K K + + +L+ + IP+E+ + E ++
Sbjct: 55 LDELKEHIEKKCKKANVDESKFIKIANLILSNVKIIPKEKYNDKSKEAYN 104
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 27.9 bits (63), Expect = 6.3
Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 7/54 (12%)
Query: 195 EKMKGQKKKLEEPWEKYDLMKEYRRTI-----PEEEQEEIFSEV--FSELHQLS 241
E++K +K+L E + D ++E R I P+E +E+ E+ + +S
Sbjct: 233 EQLKAIQKELGEDDDDKDEVEELREKIEKLKLPKEAKEKAEKELKKLETMSPMS 286
>gnl|CDD|225949 COG3415, COG3415, Transposase and inactivated derivatives [DNA
replication, recombination, and repair].
Length = 138
Score = 27.0 bits (60), Expect = 6.9
Identities = 14/88 (15%), Positives = 28/88 (31%), Gaps = 3/88 (3%)
Query: 174 WVGRWERKGYKGIDDVDQHITEKMKGQKKKLEEPWEKYDLMKEYRRTIPEEEQEEIF--- 230
WV R+ G + K+ ++ ++ + + ++
Sbjct: 41 WVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLREKDWTLKELVEELGLEFGVWYHA 100
Query: 231 SEVFSELHQLSLSNKKLKKSRVYVKPKK 258
S V LH+L LS KK + +
Sbjct: 101 SAVRRLLHELGLSYKKPRWTPAERDEPA 128
>gnl|CDD|173865 cd08500, PBP2_NikA_DppA_OppA_like_4, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 499
Score = 27.6 bits (62), Expect = 7.9
Identities = 8/44 (18%), Positives = 20/44 (45%), Gaps = 3/44 (6%)
Query: 198 KGQKKKLEEPWEK--YDLMKEYRRTIPEEEQEEIFSEVFSELHQ 239
PWEK DL + + +E+++ +++E+ ++
Sbjct: 433 GPPGGPEPPPWEKKIDDLYDKGAVELDQEKRKALYAEIQ-KIAA 475
>gnl|CDD|218899 pfam06102, DUF947, Domain of unknown function (DUF947). Family of
eukaryotic proteins with unknown function.
Length = 168
Score = 26.9 bits (60), Expect = 8.5
Identities = 26/83 (31%), Positives = 42/83 (50%), Gaps = 10/83 (12%)
Query: 180 RKGYKGIDDVDQHITEKMKGQKKKLEEPWEKYDL------MKEYRRTIPEEEQE-EIFSE 232
RK YK +DD + E+++ KK ++ EK +L MK +T+ +++E EI E
Sbjct: 51 RKNYKFLDDYREKEIEELEKALKKTKDSEEKEELKRTLQSMKSRLKTLKNKDREREILKE 110
Query: 233 VFSELHQLSLSNKK---LKKSRV 252
+ +L KK LKKS +
Sbjct: 111 HKKQEKELIKEGKKPYYLKKSEI 133
>gnl|CDD|218410 pfam05065, Phage_capsid, Phage capsid family. Family of
bacteriophage hypothetical proteins and capsid proteins.
Length = 240
Score = 26.9 bits (60), Expect = 9.1
Identities = 9/33 (27%), Positives = 14/33 (42%), Gaps = 2/33 (6%)
Query: 56 VVDNLGIEIAY--DLYDPTIHNITVLRLEKRLD 86
+VD G+ + D Y N R +R+D
Sbjct: 194 IVDREGVTVERLRDPYTAFEKNQVGFRATERVD 226
>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 = 27.3 bits (61), Expect = 9.2
Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 8/32 (25%)
Query: 215 KEYRRT--------IPEEEQEEIFSEVFSELH 238
+EY T I EEEQ+ IF V + LH
Sbjct: 236 EEYLATRRAMDVVGISEEEQDAIFRVVAAILH 267
>gnl|CDD|227610 COG5290, COG5290, IkappaB kinase complex, IKAP component
[Transcription].
Length = 1243
Score = 27.7 bits (61), Expect = 9.3
Identities = 28/130 (21%), Positives = 48/130 (36%), Gaps = 9/130 (6%)
Query: 46 GLRH-EFVLRNVVDNLGIEIAYDLYDPTIHNITVLRLEKRLDDDL-LYLRDALPNVVDNL 103
GLRH EF LR D ++L + L+ + YL+ +
Sbjct: 282 GLRHGEFDLRVGCDEKAFLENWNLLSTVLAVAEGNLLKLWTTKNYHWYLKVER-QIPGI- 339
Query: 104 GIEIAYDMYDPTIHNITVLRLEKRLDDDLLYLRDALPQYSTFPFDMEPEYLLDGAPVPIN 163
+Y + P N + R +R+ + S +PFD Y++DG+ +
Sbjct: 340 ----SYVKWHPEEKNTLLFRDGERILRVFFSEKKT-HHGSEYPFDNGTSYVIDGSYMLYT 394
Query: 164 DIKVKLKPRP 173
+ +K P P
Sbjct: 395 PLSLKNLPPP 404
>gnl|CDD|179392 PRK02249, PRK02249, DNA primase large subunit; Validated.
Length = 343
Score = 27.2 bits (61), Expect = 9.4
Identities = 12/41 (29%), Positives = 17/41 (41%)
Query: 48 RHEFVLRNVVDNLGIEIAYDLYDPTIHNITVLRLEKRLDDD 88
+ LR + +LGI + +H LRL RL D
Sbjct: 105 EPDDDLRELARDLGIPARVEGDGFAVHVTDYLRLAARLKDP 145
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
0.320 0.141 0.418
Gapped
Lambda K H
0.267 0.0778 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,199,923
Number of extensions: 1456820
Number of successful extensions: 1605
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1599
Number of HSP's successfully gapped: 66
Length of query: 260
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 165
Effective length of database: 6,723,972
Effective search space: 1109455380
Effective search space used: 1109455380
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 (21.7 bits)
S2: 58 (26.0 bits)