RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9555
(138 letters)
>gnl|CDD|217325 pfam03028, Dynein_heavy, Dynein heavy chain and region D6 of dynein
motor. This family represents the C-terminal region of
dynein heavy chain. The chain also contains ATPase
activity and microtubule binding ability and acts as a
motor for the movement of organelles and vesicles along
microtubules. Dynein is also involved in cilia and
flagella movement. The dynein subunit consists of at
least two heavy chains and a number of intermediate and
light chains. The 380 kDa motor unit of dynein belongs
to the AAA class of chaperone-like ATPases. The core of
the 380 kDa motor unit contains a concatenated chain of
six AAA modules, of which four correspond to the ATP
binding sites with P-loop signatures described
previously, and two are modules in which the P loop has
been lost in evolution. This C-terminal domain carries
the D6 region of the dynein motor where the P-loop has
been lost in evolution but the general structure of a
potential ATP binding site appears to be retained.
Length = 706
Score = 78.5 bits (194), Expect = 6e-18
Identities = 33/114 (28%), Positives = 59/114 (51%), Gaps = 18/114 (15%)
Query: 16 PMNIFLRQEIDRIQRVILEVRKTLTDLKLAIDGTITGNKFSSLICPSIQSIVMSQGLKSS 75
P+ L QEI+R+ +++ E+R++L +L L + G +T M+ L+
Sbjct: 470 PLFRVLFQEIERMNKLLKEIRRSLKELDLGLKGELT----------------MTNDLEDL 513
Query: 76 LDAMYDARIPEKWQKISWES-ATLGFWYTELLERDIQFRRWYQH-GRPNVFWMT 127
A++ R+P W K+++ S LG W T+LL R Q + W + G+P W++
Sbjct: 514 AKALFKGRVPASWAKLAYPSLKPLGSWVTDLLRRIRQLQDWTEDFGKPKTVWLS 567
>gnl|CDD|236117 PRK07857, PRK07857, hypothetical protein; Provisional.
Length = 106
Score = 29.3 bits (66), Expect = 0.28
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 21 LRQEIDRIQRVILEVRKTLTDLKLAI 46
LR+EIDR+ IL + K T++ AI
Sbjct: 33 LREEIDRLDAEILALVKRRTEVSQAI 58
>gnl|CDD|225419 COG2864, FdnI, Cytochrome b subunit of formate dehydrogenase
[Energy production and conversion].
Length = 218
Score = 28.5 bits (64), Expect = 1.1
Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 5/58 (8%)
Query: 55 FSSLICPSIQSIVMSQGLKSSLDAMYDARIPEKWQKISWESATLGFWYTELLERDIQF 112
LI I I M+ +K S+ M + ++ E W K WY E+++ +I+
Sbjct: 160 AVILIFIIIVHIYMAFWVKGSIRGMVEGKVTETWAKKH-----HPRWYREVVKGEIER 212
>gnl|CDD|232804 TIGR00064, ftsY, signal recognition particle-docking protein FtsY.
There is a weak division between FtsY and SRP54; both
are GTPases. In E.coli, ftsY is an essential gene
located in an operon with cell division genes ftsE and
ftsX, but its apparent function is as the signal
recognition particle docking protein [Protein fate,
Protein and peptide secretion and trafficking].
Length = 272
Score = 28.4 bits (64), Expect = 1.2
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 21 LRQEIDRIQRVILEVRKTLTDLK-LAIDGTITGN 53
L E+ +I+RVI +V K D L +D T TG
Sbjct: 172 LMDELKKIKRVIKKVDKDAPDEVLLVLDAT-TGQ 204
>gnl|CDD|176463 cd01359, Argininosuccinate_lyase, Argininosuccinate lyase
(argininosuccinase, ASAL). This group contains ASAL 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. ASAL is a cytosolic enzyme which catalyzes the
reversible breakdown of argininosuccinate to arginine
and fumarate during arginine biosynthesis. In ureotelic
species ASAL also catalyzes a reaction involved in the
production of urea. Included in this group are the major
soluble avian eye lens proteins from duck, delta 1 and
delta 2 crystallin. Of these two isoforms only delta 2
has retained ASAL activity. These crystallins may have
evolved by, gene recruitment of ASAL followed by gene
duplication. In humans, mutations in ASAL result in the
autosomal recessive disorder argininosuccinic aciduria.
Length = 435
Score = 28.3 bits (64), Expect = 1.5
Identities = 5/24 (20%), Positives = 15/24 (62%)
Query: 19 IFLRQEIDRIQRVILEVRKTLTDL 42
++LR + + ++L++++ L D
Sbjct: 97 LYLRDALLELLELLLDLQRALLDR 120
>gnl|CDD|179143 PRK00855, PRK00855, argininosuccinate lyase; Provisional.
Length = 459
Score = 28.2 bits (64), Expect = 1.6
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 20 FLRQEIDRIQRVILEVRKTLTDL 42
+LR EID I ++LE++K L DL
Sbjct: 122 YLRDEIDEIAELLLELQKALLDL 144
>gnl|CDD|217451 pfam03249, TSA, Type specific antigen. There are several antigenic
variants in Rickettsia tsutsugamushi, and a
type-specific antigen (TSA) of 56-kilodaltons located on
the rickettsial surface is responsible for the
variation. TSA proteins are probably integral membrane
proteins.
Length = 502
Score = 27.9 bits (62), Expect = 1.8
Identities = 12/35 (34%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 25 IDRIQRVILEVRKTLTDLKLAIDGTITGNKFSSLI 59
+++IQ + E+ L +L+ + DG I GN F++ I
Sbjct: 267 VEQIQNKMQELNDVLEELRESFDGYI-GNAFANQI 300
>gnl|CDD|146285 pfam03566, Peptidase_A21, Peptidase family A21.
Length = 628
Score = 28.0 bits (62), Expect = 2.0
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 108 RDIQFRRWYQHGRPNVFWMTTRVTQNTYS 136
RD +W Q +++ RV TY+
Sbjct: 198 RDADSPQWAQFSDDPTWYVRIRVLHPTYA 226
>gnl|CDD|212052 cd11483, SLC-NCS1sbd_Mhp1-like, nucleobase-cation-symport-1 (NCS1)
transporter Mhp1-like; solute-binding domain. This NCS1
subfamily includes Microbacterium liquefaciens Mhp1, and
various uncharacterized NCS1s. Mhp1 mediates the uptake
of indolyl methyl- and benzyl-hydantoins as part of a
metabolic salvage pathway for their conversion to amino
acids. Mhp1 has 12 transmembrane (TM) helices (an
inverted topology repeat: TMs1-5 and TMs6-10, and
TMs11-12; TMs numbered to conform to the Solute carrier
6 (SLC6) family Aquifex aeolicus LeuT). NCS1s are
essential components of salvage pathways for nucleobases
and related metabolites; their other known substrates
include allantoin, uracil, thiamine, and nicotinamide
riboside. NCS1s belong to a superfamily which also
contains the solute carrier 5 family sodium/glucose
transporters (SLC5s), and SLC6 neurotransmitter
transporters.
Length = 434
Score = 27.6 bits (62), Expect = 2.4
Identities = 13/82 (15%), Positives = 27/82 (32%), Gaps = 20/82 (24%)
Query: 54 KFSSLICPSIQSIVMSQGLKSSLDAMYDARIPEKW--QKISWE-------SATLGFW--- 101
++ P I I + + +L Y I E + +W A +G W
Sbjct: 155 WLENIAAPVI--IAILVYMFYTLLTKYGVSIGENLWSFEGTWGMPFWAAIMAFMGGWSTM 212
Query: 102 ------YTELLERDIQFRRWYQ 117
Y+ L+ + +++
Sbjct: 213 ALNIPDYSRELKPGPNYEGFFK 234
>gnl|CDD|223243 COG0165, ArgH, Argininosuccinate lyase [Amino acid transport and
metabolism].
Length = 459
Score = 27.2 bits (61), Expect = 3.0
Identities = 7/29 (24%), Positives = 16/29 (55%)
Query: 17 MNIFLRQEIDRIQRVILEVRKTLTDLKLA 45
+ ++LR ++ + +I ++K L DL
Sbjct: 118 LRLWLRDKLLELLELIRILQKALLDLAEE 146
>gnl|CDD|237585 PRK14015, pepN, aminopeptidase N; Provisional.
Length = 875
Score = 27.4 bits (62), Expect = 3.2
Identities = 12/18 (66%), Positives = 13/18 (72%), Gaps = 2/18 (11%)
Query: 108 RDI-QFRRWY-QHGRPNV 123
RD+ QFRRWY Q G P V
Sbjct: 436 RDLSQFRRWYSQAGTPRV 453
>gnl|CDD|237693 PRK14368, PRK14368, Maf-like protein; Provisional.
Length = 193
Score = 26.7 bits (59), Expect = 3.5
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 1 MCSVREALQRMGALL 15
+C V EAL+ +GAL
Sbjct: 179 LCEVVEALRTIGALG 193
>gnl|CDD|217151 pfam02624, YcaO, YcaO-like family.
Length = 332
Score = 26.9 bits (60), Expect = 3.8
Identities = 10/31 (32%), Positives = 14/31 (45%), Gaps = 3/31 (9%)
Query: 92 SWESATL-GFWYTELLERDIQFRRWYQHGRP 121
+ E A L G E++ERD + WY
Sbjct: 121 TLEEAILHGLL--EVIERDAKALAWYNRLPL 149
>gnl|CDD|130867 TIGR01808, CM_M_hiGC-arch, monofunctional chorismate mutase, high
GC gram positive type. This model represents the
monofunctional chorismate mutase from high GC
gram-positive bacteria and archaea. Trusted annotations
from Corynebacterium and Pyrococcus are aparrently the
sole chorismate mutase enzymes in their respective
genomes. This is coupled with the presence in those
genomes of the enzymes of the chorismate pathways both
up- and downstream of chorismate mutase [Amino acid
biosynthesis, Aromatic amino acid family].
Length = 74
Score = 25.6 bits (56), Expect = 4.6
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 7/37 (18%)
Query: 21 LRQEIDRIQRVIL-------EVRKTLTDLKLAIDGTI 50
LR+EIDR+ IL E+ + + ++A GT
Sbjct: 5 LREEIDRLDAEILALVKRRAEISQAIGKARMASGGTR 41
>gnl|CDD|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR). This
family consists of several bovine specific leukaemia
virus receptors which are thought to function as
transmembrane proteins, although their exact function is
unknown.
Length = 561
Score = 26.6 bits (58), Expect = 5.0
Identities = 10/15 (66%), Positives = 13/15 (86%)
Query: 62 SIQSIVMSQGLKSSL 76
+IQSIVM+Q LK +L
Sbjct: 415 TIQSIVMAQKLKGTL 429
>gnl|CDD|224644 COG1730, GIM5, Predicted prefoldin, molecular chaperone
implicated in de novo protein folding
[Posttranslational modification, protein turnover,
chaperones].
Length = 145
Score = 26.2 bits (58), Expect = 5.3
Identities = 7/38 (18%), Positives = 17/38 (44%), Gaps = 3/38 (7%)
Query: 6 EALQRMGALLPMNIFLRQEIDRIQRVILEVRKTLTDLK 43
LQ + + + L+ +I + I E++ + L+
Sbjct: 13 AQLQILQSQIES---LQAQIAALNAAISELQTAIETLE 47
>gnl|CDD|239153 cd02752, MopB_Formate-Dh-Na-like, Formate dehydrogenase N, alpha
subunit (Formate-Dh-Na) is a major component of nitrate
respiration in bacteria such as in the E. coli formate
dehydrogenase N (Fdh-N). Fdh-N is a membrane protein
that is a complex of three different subunits and is
the major electron donor to the nitrate respiratory
chain. Also included in this CD is the Desulfovibrio
gigas tungsten formate dehydrogenase, DgW-FDH. In
contrast to Fdh-N, which is a functional heterotrimer,
DgW-FDH is a heterodimer. The DgW-FDH complex is
composed of a large subunit carrying the W active site
and one [4Fe-4S] center, and a small subunit that
harbors a series of three [4Fe-4S] clusters as well as
a putative vacant binding site for a fourth cluster.
The smaller subunit is not included in this alignment.
Members of the MopB_Formate-Dh-Na-like CD belong to the
molybdopterin_binding (MopB) superfamily of proteins.
Length = 649
Score = 26.6 bits (59), Expect = 5.3
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 78 AMYDARIPEKWQKISWESA 96
MY A KW++ISW+ A
Sbjct: 58 PMYRAPGSGKWEEISWDEA 76
>gnl|CDD|235179 PRK03947, PRK03947, prefoldin subunit alpha; Reviewed.
Length = 140
Score = 25.7 bits (57), Expect = 7.0
Identities = 10/48 (20%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 1 MCSVREALQRMGALLPMNIFLRQEIDRIQRVILEVRKTLTDLKLAIDG 48
M + L+ + A L L+ +I+ +Q+ + E++ ++ +L A +
Sbjct: 1 MMESEQELEELAAQLQA---LQAQIEALQQQLEELQASINELDTAKET 45
>gnl|CDD|216597 pfam01601, Corona_S2, Coronavirus S2 glycoprotein. The coronavirus
spike glycoprotein forms the characteristic 'corona'
after which the group is named. The Spike glycoprotein
is translated as a large polypeptide that is
subsequently cleaved to S1 pfam01600 and S2.
Length = 609
Score = 26.1 bits (58), Expect = 7.3
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 21 LRQEIDRIQRVILEVRKTLTDLK 43
L EIDR+Q VI + +L DL+
Sbjct: 512 LTGEIDRLQEVIKNLNDSLIDLE 534
>gnl|CDD|237973 PRK15488, PRK15488, thiosulfate reductase PhsA; Provisional.
Length = 759
Score = 26.2 bits (58), Expect = 7.8
Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 7/33 (21%)
Query: 87 KWQKISWESATLGFWYTELLERDIQFRRWYQHG 119
KWQ+ISW+ A Y E+ + ++ QHG
Sbjct: 113 KWQEISWDEA-----YQEIAAKLNAIKQ--QHG 138
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 25.7 bits (56), Expect = 8.6
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 11 MGALLPMNIFLRQEIDRIQRVILEVR 36
+GALL +I RQ D +QR + E+R
Sbjct: 86 VGALLVYDITKRQTFDNVQRWLRELR 111
>gnl|CDD|239160 cd02759, MopB_Acetylene-hydratase, The MopB_Acetylene-hydratase CD
contains acetylene hydratase (Ahy) and other related
proteins. The acetylene hydratase of Pelobacter
acetylenicus is a tungsten iron-sulfur protein involved
in the fermentation of acetylene to ethanol and acetate.
Members of this CD belong to the molybdopterin_binding
(MopB) superfamily of proteins.
Length = 477
Score = 25.7 bits (57), Expect = 9.2
Identities = 11/51 (21%), Positives = 19/51 (37%), Gaps = 13/51 (25%)
Query: 87 KWQKISWESATLGFWYTELLERDIQFRRWY-------QHGRP-NVFWMTTR 129
KW++ISW+ A E+ E+ + + Y G W +
Sbjct: 69 KWERISWDEA-----LDEIAEKLAEIKAEYGPESIATAVGTGRGTMWQDSL 114
>gnl|CDD|223321 COG0243, BisC, Anaerobic dehydrogenases, typically
selenocysteine-containing [Energy production and
conversion].
Length = 765
Score = 25.9 bits (57), Expect = 9.2
Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 82 ARIPEKWQKISWESATLGFWYTELLERDIQF 112
R K+ +ISW+ A +LL R I F
Sbjct: 108 KRGEGKFVRISWDEALDLI-AAKLLPRIIGF 137
>gnl|CDD|189007 cd09600, M1_APN_1, Peptidase M1 family containing Aminopeptidase N.
This family contains aminopeptidase N (APN; CD13;
Alanyl aminopeptidase; EC 3.4.11.2), a Type II integral
membrane protease belonging to the M1 gluzincin family.
It includes bacterial-type alanyl aminopeptidases as
well as PfA-M1 aminopeptidase (Plasmodium
falciparum-type). APN consists of a small N-terminal
cytoplasmic domain, a single transmembrane domain and a
large extracellular ectodomain that contains the active
site. It preferentially cleaves neutral amino acids from
the N-terminus of oligopeptides and, in higher
eukaryotes, is present in a variety of human tissues and
cell types (leukocyte, fibroblast, endothelial and
epithelial cells). APN expression is dysregulated in
inflammatory diseases such as chronic pain, rheumatoid
arthritis, multiple sclerosis, systemic sclerosis,
systemic lupus erythematosus,
polymyositis/dermatomyosytis and pulmonary sarcoidosis,
and is enhanced in tumor cells such as melanoma, renal,
prostate, pancreas, colon, gastric and thyroid cancers.
It is predominantly expressed on stem cells and on cells
of the granulocytic and monocytic lineages at distinct
stages of differentiation, thus considered a marker of
differentiation. Thus, APN inhibition may lead to the
development of anti-cancer and anti-inflammatory drugs.
APNs are also present in many pathogenic bacteria and
represent potential drug targets, Some APNs have been
used commercially, such as one from Lactococcus lactis
used in the food industry. APN also serves as a receptor
for coronaviruses, although the virus receptor
interaction site seems to be distinct from the enzymatic
site and aminopeptidase activity is not necessary for
viral infection. APNs have also been extensively studied
as putative Cry toxin receptors. Cry1 proteins are
pore-forming toxins that bind to the midgut epithelial
cell membrane of susceptible insect larvae, causing
extensive damage. Several different toxins, including
Cry1Aa, Cry1Ab, Cry1Ac, Cry1Ba, Cry1Ca and Cry1Fa, have
been shown to bind to APNs; however, a direct role of
APN in cytotoxicity has been yet to be firmly
established.
Length = 861
Score = 25.7 bits (57), Expect = 9.6
Identities = 11/19 (57%), Positives = 12/19 (63%), Gaps = 2/19 (10%)
Query: 107 ERDI-QFRRWY-QHGRPNV 123
D+ QFRRWY Q G P V
Sbjct: 422 GVDLSQFRRWYSQAGTPKV 440
>gnl|CDD|221737 pfam12726, SEN1_N, SEN1 N terminal. This domain is found at the N
terminal of the helicase SEN1. SEN1 is a Pol II
termination factor for noncoding RNA genes. The N
terminal of SEN1, unlike the C terminal, is not required
for growth.
Length = 724
Score = 25.7 bits (57), Expect = 9.8
Identities = 18/99 (18%), Positives = 37/99 (37%), Gaps = 4/99 (4%)
Query: 17 MNIFLRQEIDRIQRVILEVRKTLTDLKLAIDGTITGNKFSSLICPSIQSIVMSQGLKSSL 76
M +I RI + + K L ++ + L P++ + L+
Sbjct: 44 MEKIDEWDIQRILPGLEKASKILESGPPNTRSSLLLALYECLCNPALLR--NDELLRELF 101
Query: 77 DAMYDARIPEKWQKISWESATLGFWYTELLERDIQFRRW 115
DA++ +K + ++ G Y L E + + R+W
Sbjct: 102 DAIFKLLQTKK-SLLLPKTLLPGLTYF-LFEGNPERRKW 138
>gnl|CDD|226599 COG4114, FhuF, Uncharacterized Fe-S protein [General function
prediction only].
Length = 251
Score = 25.6 bits (56), Expect = 10.0
Identities = 11/53 (20%), Positives = 19/53 (35%), Gaps = 13/53 (24%)
Query: 90 KISWE-SATLGFWY---------TELLERDIQ---FRRWYQHGRPNVFWMTTR 129
++ W + L WY +L+E F + +G+ N W T
Sbjct: 169 RLLWNNTGYLINWYLTEMKQLLGEDLVESLRHALFFEKLLPNGQDNPLWRTVV 221
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
0.323 0.134 0.413
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,017,273
Number of extensions: 608371
Number of successful extensions: 874
Number of sequences better than 10.0: 1
Number of HSP's gapped: 872
Number of HSP's successfully gapped: 38
Length of query: 138
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 51
Effective length of database: 7,078,804
Effective search space: 361019004
Effective search space used: 361019004
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (24.6 bits)