RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 033150
(126 letters)
>gnl|CDD|235358 PRK05179, rpsM, 30S ribosomal protein S13; Validated.
Length = 122
Score = 96.3 bits (241), Expect = 6e-27
Identities = 34/69 (49%), Positives = 50/69 (72%), Gaps = 2/69 (2%)
Query: 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKM-ENKITKDMSEEELITIRDEVS 106
AR+ GV+IP NKR+ +L YI+G+GRTRA++IL + + KD+++EEL IR+E+
Sbjct: 2 ARIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEID 61
Query: 107 K-YMIEGDL 114
K Y +EGDL
Sbjct: 62 KNYKVEGDL 70
>gnl|CDD|213840 TIGR03631, bact_S13, 30S ribosomal protein S13. This model
describes bacterial ribosomal protein S13, to the
exclusion of the homologous archaeal S13P and eukaryotic
ribosomal protein S18. This model identifies some (but
not all) instances of chloroplast and mitochondrial S13,
which is of bacterial type [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 113
Score = 92.6 bits (231), Expect = 1e-25
Identities = 38/68 (55%), Positives = 53/68 (77%), Gaps = 2/68 (2%)
Query: 49 RVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKM-ENKITKDMSEEELITIRDEV-S 106
R+ GV+IPNNKR+E +L YI+G+GRTRAR+IL + +K KD++EEEL IR+E+ +
Sbjct: 1 RIAGVDIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEIEA 60
Query: 107 KYMIEGDL 114
KY +EGDL
Sbjct: 61 KYKVEGDL 68
>gnl|CDD|223177 COG0099, RpsM, Ribosomal protein S13 [Translation, ribosomal
structure and biogenesis].
Length = 121
Score = 88.4 bits (220), Expect = 6e-24
Identities = 30/69 (43%), Positives = 49/69 (71%), Gaps = 2/69 (2%)
Query: 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKM-ENKITKDMSEEELITIRDEV- 105
AR+ GV+IP NKR+ +L YI+G+GR RA++I + +K +++EEE+ +RD +
Sbjct: 2 ARIAGVDIPGNKRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAIQ 61
Query: 106 SKYMIEGDL 114
+KY++EGDL
Sbjct: 62 NKYLVEGDL 70
>gnl|CDD|144128 pfam00416, Ribosomal_S13, Ribosomal protein S13/S18. This family
includes ribosomal protein S13 from prokaryotes and S18
from eukaryotes.
Length = 106
Score = 87.7 bits (218), Expect = 8e-24
Identities = 27/67 (40%), Positives = 43/67 (64%), Gaps = 1/67 (1%)
Query: 49 RVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKM-ENKITKDMSEEELITIRDEVSK 107
R+ + NK+IE +L YI G+GR +A QIL + ++K +++EEE+ IRD +S
Sbjct: 1 RILNTNLDGNKKIEIALTYIKGIGRRKANQILKKAGVDKDKRVGELTEEEIDRIRDIISN 60
Query: 108 YMIEGDL 114
Y++E DL
Sbjct: 61 YVVENDL 67
>gnl|CDD|177059 CHL00137, rps13, ribosomal protein S13; Validated.
Length = 122
Score = 73.9 bits (182), Expect = 3e-18
Identities = 29/69 (42%), Positives = 49/69 (71%), Gaps = 2/69 (2%)
Query: 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEV- 105
R+ GV++P NKRIEY+L YI+G+G T A++IL ++ + TKD+++E++ +R+ +
Sbjct: 2 VRIAGVDLPRNKRIEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISALREIIE 61
Query: 106 SKYMIEGDL 114
Y +EGDL
Sbjct: 62 ENYQVEGDL 70
>gnl|CDD|235215 PRK04053, rps13p, 30S ribosomal protein S13P; Reviewed.
Length = 149
Score = 40.2 bits (95), Expect = 4e-05
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 49 RVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVS 106
R+ G ++ K +EY+L I G+GR AR I L ++ N +S+EE+ I + +
Sbjct: 11 RIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALE 69
>gnl|CDD|213839 TIGR03629, arch_S13P, archaeal ribosomal protein S13P. This model
describes exclusively the archaeal ribosomal protein
S13P. It excludes the homologous eukaryotic 40S
ribosomal protein S18 and bacterial 30S ribosomal
protein S13 [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 144
Score = 40.0 bits (94), Expect = 4e-05
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 49 RVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK 107
R+ ++ NK +EY+L I G+GR AR I L ++ N + +EE+ + + V
Sbjct: 7 RIADTDLDGNKPVEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAVEN 66
Query: 108 Y 108
Y
Sbjct: 67 Y 67
>gnl|CDD|219216 pfam06883, RNA_pol_Rpa2_4, RNA polymerase I, Rpa2 specific
domain. This domain is found between domain 3
(pfam04565) and domain 5 (pfam04565), but shows no
homology to domain 4 of Rpb2. The external domains in
multisubunit RNA polymerase (those most distant from
the active site) are known to demonstrate more sequence
variability.
Length = 58
Score = 26.4 bits (59), Expect = 1.3
Identities = 9/19 (47%), Positives = 10/19 (52%), Gaps = 2/19 (10%)
Query: 33 PVSKQPQYPGLSI--QCAR 49
P S QYPGL + AR
Sbjct: 37 PPSNGGQYPGLYLFSTPAR 55
>gnl|CDD|235807 PRK06460, PRK06460, hypothetical protein; Provisional.
Length = 376
Score = 27.5 bits (61), Expect = 1.9
Identities = 12/50 (24%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 1 MVQTLAMPV-----APALSVICNGHNNNLLTNASLSFPVSKQPQYPGLSI 45
V+ + P+ LS +C + + L+ +A+ S P++++P G I
Sbjct: 135 FVENITNPLLRVVDITELSKVCKENGSILIVDATFSTPINQKPLELGADI 184
>gnl|CDD|240391 PTZ00377, PTZ00377, alanine aminotransferase; Provisional.
Length = 481
Score = 27.6 bits (62), Expect = 1.9
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 38 PQYPGLSIQCARVGGVEIP 56
PQYP S +GG ++P
Sbjct: 171 PQYPLYSAAITLLGGKQVP 189
>gnl|CDD|217035 pfam02441, Flavoprotein, Flavoprotein. This family contains
diverse flavoprotein enzymes. This family includes
epidermin biosynthesis protein, EpiD, which has been
shown to be a flavoprotein that binds FMN. This enzyme
catalyzes the removal of two reducing equivalents from
the cysteine residue of the C-terminal meso-lanthionine
of epidermin to form a --C==C-- double bond. This family
also includes the B chain of dipicolinate synthase a
small polar molecule that accumulates to high
concentrations in bacterial endospores, and is thought
to play a role in spore heat resistance, or the
maintenance of heat resistance. dipicolinate synthase
catalyzes the formation of dipicolinic acid from
dihydroxydipicolinic acid. This family also includes
phenyl-acrylic acid decarboxylase (EC:4.1.1.-).
Length = 132
Score = 26.8 bits (60), Expect = 2.1
Identities = 16/37 (43%), Positives = 22/37 (59%), Gaps = 4/37 (10%)
Query: 6 AMPVAPA----LSVICNGHNNNLLTNASLSFPVSKQP 38
M VAPA L+ I NG +NLLT A+L+ ++P
Sbjct: 79 LMVVAPATANTLAKIANGIADNLLTRAALAALKERKP 115
>gnl|CDD|238332 cd00591, HU_IHF, Integration host factor (IHF) and HU are small
heterodimeric members of the DNABII protein family that
bind and bend DNA, functioning as architectural factors
in many cellular processes including transcription,
site-specific recombination, and higher-order
nucleoprotein complex assembly. The dimer subunits
associate to form a compact globular core from which two
beta ribbon arms (one from each subunit) protrude. The
beta arms track and bind the DNA minor groove. Despite
sequence and structural similarity, IHF and HU can be
distinguished by their different DNA substrate
preferences.
Length = 87
Score = 26.3 bits (59), Expect = 2.6
Identities = 11/48 (22%), Positives = 26/48 (54%), Gaps = 4/48 (8%)
Query: 80 LVD-LKMENKITKDMSEEELITIRDEVSKYMIEGDLVIIPYFFVRGTF 126
L++ + + ++K +E + D +++ + +G+ V +P F GTF
Sbjct: 5 LIEAIAEKTGLSKKDAEAAVDAFLDVITEALAKGEKVELPGF---GTF 49
>gnl|CDD|232867 TIGR00194, uvrC, excinuclease ABC, C subunit. This family consists
of the DNA repair enzyme UvrC, an ABC excinuclease
subunit which interacts with the UvrA/UvrB complex to
excise UV-damaged nucleotide segments [DNA metabolism,
DNA replication, recombination, and repair].
Length = 574
Score = 27.3 bits (61), Expect = 2.6
Identities = 12/40 (30%), Positives = 17/40 (42%), Gaps = 1/40 (2%)
Query: 58 NKRIEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEE 97
++ L I GVG R +++L I K S EE
Sbjct: 536 KASLQSPLLKIPGVGEKRVQKLLKYFGSLKGI-KKASVEE 574
>gnl|CDD|236111 PRK07843, PRK07843, 3-ketosteroid-delta-1-dehydrogenase;
Reviewed.
Length = 557
Score = 26.9 bits (60), Expect = 3.2
Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 13/48 (27%)
Query: 34 VSKQPQYPGLSIQCARVG-GVEIPNNK---------RIEYSLQYIHGV 71
V K P Y G + AR G GV IPNN+ E + Y+H +
Sbjct: 36 VEKAPHYGGST---ARSGGGVWIPNNEVLKRAGVPDTPEAARTYLHSI 80
>gnl|CDD|240629 cd05304, Rubrum_tdh, Rubrum transdehydrogenase NAD-binding and
catalytic domains. Transhydrogenases found in bacterial
and inner mitochondrial membranes link
NAD(P)(H)-dependent redox reactions to proton
translocation. The energy of the proton electrochemical
gradient (delta-p), generated by the respiratory
electron transport chain, is consumed by
transhydrogenase in NAD(P)+ reduction. Transhydrogenase
is likely involved in the regulation of the citric acid
cycle. Rubrum transhydrogenase has 3 components, dI,
dII, and dIII. dII spans the membrane while dI and dIII
protrude on the cytoplasmic/matrix side. DI contains 2
domains in Rossmann-like folds, linked by a long alpha
helix, and contains a NAD binding site. Two dI
polypeptides (represented in this sub-family)
spontaneously form a heterotrimer with dIII in the
absence of dII. In the heterotrimer, both dI chains may
bind NAD, but only one is well-ordered. dIII also binds
a well-ordered NADP, but in a different orientation than
a classical Rossmann domain.
Length = 363
Score = 26.6 bits (60), Expect = 4.4
Identities = 13/32 (40%), Positives = 21/32 (65%), Gaps = 4/32 (12%)
Query: 91 KDMSEEELITIRDEVSKYMIEGDLVI----IP 118
K++SEE L R+ ++K++ E D+VI IP
Sbjct: 229 KELSEEFLAKQRELLAKHIAEADIVITTALIP 260
>gnl|CDD|180281 PRK05839, PRK05839, hypothetical protein; Provisional.
Length = 374
Score = 26.2 bits (58), Expect = 5.3
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 11/43 (25%)
Query: 75 RARQILVDLKMENKITKDMSEEELITIRDEVSKYMIEGDLVII 117
RA+ +L+ L EN T ++E+EL E DLVI+
Sbjct: 130 RAKVLLMPLTKENDFTPSLNEKEL-----------QEVDLVIL 161
>gnl|CDD|223852 COG0781, NusB, Transcription termination factor [Transcription].
Length = 151
Score = 25.7 bits (57), Expect = 6.4
Identities = 12/58 (20%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 72 GRTRARQILVDLKMENKITKDMSEEELITIR-DEVSKYMIEGDLVIIPYF--FVRGTF 126
R +AR++ V + +++ +S E+++ +E + ++ +L YF V+G
Sbjct: 9 TRRQARELAVQALYQWELSGSVSAEDILEDIEEEFVENELDIELADSEYFRSLVKGVL 66
>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 = 26.1 bits (58), Expect = 6.6
Identities = 8/21 (38%), Positives = 15/21 (71%)
Query: 88 KITKDMSEEELITIRDEVSKY 108
KI K +++E+ I RD ++K+
Sbjct: 320 KIVKPLTKEQAIVARDALAKH 340
>gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed.
Length = 1112
Score = 25.8 bits (58), Expect = 7.9
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 14/55 (25%)
Query: 72 GRTRARQILVDLKMENKITKDMSEEELITIRDEVSKYMIEGDLVIIPYFFVRGTF 126
G T + + V L++ NK T ++ E+E+ YM GD IP GTF
Sbjct: 90 GLTYSAPLRVKLRLINKETGEIKEQEV---------YM--GD---IPLMTENGTF 130
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 25.6 bits (57), Expect = 9.0
Identities = 8/36 (22%), Positives = 22/36 (61%)
Query: 78 QILVDLKMENKITKDMSEEELITIRDEVSKYMIEGD 113
+ L +L + I+ D+S++EL+ ++ ++ + + D
Sbjct: 237 KKLKELGVIVSISPDVSKKELLGLQKKLQQEIANDD 272
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
0.321 0.137 0.394
Gapped
Lambda K H
0.267 0.0789 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,283,639
Number of extensions: 545011
Number of successful extensions: 598
Number of sequences better than 10.0: 1
Number of HSP's gapped: 590
Number of HSP's successfully gapped: 39
Length of query: 126
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 41
Effective length of database: 7,167,512
Effective search space: 293867992
Effective search space used: 293867992
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 (21.8 bits)
S2: 53 (24.1 bits)