RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780470|ref|YP_003064883.1| translation initiation factor
IF-1 [Candidatus Liberibacter asiaticus str. psy62]
(110 letters)
>gnl|CDD|88417 cd04451, S1_IF1, S1_IF1: Translation Initiation Factor IF1, S1-like
RNA-binding domain. IF1 contains an S1-like RNA-binding
domain, which is found in a wide variety of
RNA-associated proteins. Translation initiation includes
a number of interrelated steps preceding the formation
of the first peptide bond. In Escherichia coli, the
initiation mechanism requires, in addition to mRNA,
fMet-tRNA, and ribosomal subunits, the presence of
three additional proteins (initiation factors IF1, IF2,
and IF3) and at least one GTP molecule. The three
initiation factors influence both the kinetics and the
stability of ternary complex formation. IF1 is the
smallest of the three factors. IF1 enhances the rate of
70S ribosome subunit association and dissociation and
the interaction of 30S ribosomal subunit with IF2 and
IF3. It stimulates 30S complex formation. In addition,
by binding to the A-site of the 30S ribosomal subunit,
IF1 may contribute to the fidelity of the selection of
the initiation site of the mRNA..
Length = 64
Score = 73.6 bits (181), Expect = 1e-14
Identities = 36/102 (35%), Positives = 51/102 (50%), Gaps = 38/102 (37%)
Query: 7 LEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLD 66
+E G+V+E LPNA FRV+L E+G E
Sbjct: 1 IEMEGVVTEALPNAMFRVEL----------------------ENGHE------------- 25
Query: 67 NAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYR 108
V+A+ +G+MR + IRI GD+VKV ++PYD+T+ RI YR
Sbjct: 26 ---VLAHISGKMRMNYIRILPGDRVKVELSPYDLTKGRIVYR 64
>gnl|CDD|176953 CHL00010, infA, translation initiation factor 1.
Length = 78
Score = 73.1 bits (180), Expect = 2e-14
Identities = 36/111 (32%), Positives = 52/111 (46%), Gaps = 40/111 (36%)
Query: 1 MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVD 60
M KE +E G+V+E LPN FRV+L
Sbjct: 1 MKKENKIEMEGLVTESLPNGMFRVRL---------------------------------- 26
Query: 61 PISYLDN-AVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK 110
DN V+ Y +G++R++ IRI GD+VKV ++PYD+T+ RI YR +
Sbjct: 27 -----DNGCQVLGYISGKIRRNSIRILPGDRVKVELSPYDLTKGRIIYRLR 72
>gnl|CDD|30710 COG0361, InfA, Translation initiation factor 1 (IF-1) [Translation,
ribosomal structure and biogenesis].
Length = 75
Score = 72.5 bits (178), Expect = 2e-14
Identities = 35/110 (31%), Positives = 50/110 (45%), Gaps = 38/110 (34%)
Query: 1 MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVD 60
M K + +E G V E+LPN FRV+L
Sbjct: 1 MAKPDEIEMEGTVIEMLPNGRFRVEL---------------------------------- 26
Query: 61 PISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK 110
+ +A+ +G+MRK+RIRI GD V V ++PYD+T+ RI YR+K
Sbjct: 27 ----ENGHERLAHISGKMRKNRIRILPGDVVLVELSPYDLTKGRIVYRYK 72
>gnl|CDD|110196 pfam01176, eIF-1a, Translation initiation factor 1A / IF-1. This
family includes both the eukaryotic translation factor
eIF-1A and the bacterial translation initiation factor
IF-1.
Length = 65
Score = 55.2 bits (134), Expect = 4e-09
Identities = 29/101 (28%), Positives = 38/101 (37%), Gaps = 39/101 (38%)
Query: 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDN 67
E G V+E+L N F V+L DG
Sbjct: 4 EMIGQVTEMLGNGRFEVEL-----------------------------EDGH-------- 26
Query: 68 AVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYR 108
+A+ G+ RK RI I GD V V ++PYD + RI YR
Sbjct: 27 -ERLAHIPGKRRK-RIWILRGDFVLVELSPYDKVKGRIIYR 65
>gnl|CDD|30879 COG0533, QRI7, Metal-dependent proteases with possible chaperone
activity [Posttranslational modification, protein
turnover, chaperones].
Length = 342
Score = 27.1 bits (60), Expect = 1.1
Identities = 10/24 (41%), Positives = 11/24 (45%)
Query: 66 DNAVVIAYTAGRMRKHRIRISLGD 89
DNA +IAY K IS D
Sbjct: 302 DNAAMIAYAGLLRYKAGRFISPLD 325
>gnl|CDD|119407 cd02696, MurNAc-LAA, N-acetylmuramoyl-L-alanine amidase or
MurNAc-LAA (also known as peptidoglycan aminohydrolase,
NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan
amidase; EC 3.5.1.28) is an autolysin that hydrolyzes
the amide bond between N-acetylmuramoyl and L-amino
acids in certain cell wall glycopeptides. These
proteins are Zn-dependent peptidases with highly
conserved residues involved in cation co-ordination.
MurNAc-LAA in this family is one of several
peptidoglycan hydrolases (PGHs) found in bacterial and
bacteriophage or prophage genomes that are involved in
the degradation of the peptidoglycan. In Escherichia
coli, there are five MurNAc-LAAs present: AmiA, AmiB,
AmiC and AmiD that are periplasmic, and AmpD that is
cytoplasmic. Three of these (AmiA, AmiB and AmiC)
belong to this family, the other two (AmiD and AmpD) do
not. E. coli AmiA, AmiB and AmiC play an important role
in cleaving the septum to release daughter cells after
cell division. In general, bacterial MurNAc-LAAs are
members of the bacterial autolytic system and carry a
signal peptide in their N-termini that allows their
transport across the cytoplasmic membrane. However, the
bacteriophage MurNAc-LAAs are endolysins since these
phage-encoded enzymes break down bacterial
peptidoglycan at the terminal stage of the phage
reproduction cycle. As opposed to autolysins, almost
all endolysins have no signal peptides and their
translocation through the cytoplasmic membrane is
thought to proceed with the help of phage-encoded holin
proteins. The amidase catalytic module is fused to
another functional module (cell wall binding module or
CWBM) either at the N- or C-terminus, which is
responsible for high affinity binding of the protein to
the cell wall..
Length = 172
Score = 27.1 bits (61), Expect = 1.2
Identities = 9/30 (30%), Positives = 16/30 (53%)
Query: 3 KEETLEFSGIVSELLPNANFRVKLITNDDD 32
K+ L + +++LL A +V L +DD
Sbjct: 24 KDINLAIALKLAKLLEAAGAKVVLTRDDDT 53
>gnl|CDD|88466 cd05791, S1_CSL4, S1_CSL4: CSL4, S1-like RNA-binding domain.
S1-like RNA-binding domains are found in a wide variety
of RNA-associated proteins. ScCSL4 protein is a subunit
of the exosome complex. The exosome plays a central role
in 3' to 5' RNA processing and degradation in eukarytes
and archaea. Its functions include the removal of
incorrectly processed RNA and the maintenance of proper
levels of mRNA, rRNA and a number of small RNA species.
In S. cerevisiae, the exosome includes nine core
components, six of which are homologous to bacterial
RNase PH. These form a hexameric ring structure. The
other three subunits (RrP4, Rrp40, and Csl4) contain an
S1 RNA binding domain and are part of the "S1 pore
structure"..
Length = 92
Score = 26.3 bits (58), Expect = 1.8
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 2/48 (4%)
Query: 62 ISYLDNAVVIAYTAGRMRKHRIRISLGDKVKV--AMNPYDMTRARITY 107
I + + G +RK IR + DKV++ P D+ RA++
Sbjct: 26 ILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVIS 73
>gnl|CDD|144931 pfam01520, Amidase_3, N-acetylmuramoyl-L-alanine amidase. This
enzyme domain cleaves the amide bond between
N-acetylmuramoyl and L-amino acids in bacterial cell
walls.
Length = 172
Score = 26.0 bits (58), Expect = 2.1
Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 3 KEETLEFSGIVSELLPNANFRVKLITNDDDSSADCK 38
K+ L+ + +++LL A V L T DDDS
Sbjct: 23 KDLNLDIALRLAKLLEAAGVEVVL-TRDDDSFVSLS 57
>gnl|CDD|107371 cd06376, PBP1_mGluR_groupIII, Ligand-binding domain of the group
III metabotropic glutamate receptor. Ligand-binding
domain of the group III metabotropic glutamate receptor,
a family which contains mGlu4R, mGluR6R, mGluR7, and
mGluR8; all of which inhibit adenylyl cyclase. The
metabotropic glutamate receptor is a member of the
family C of G-protein-coupled receptors that transduce
extracellular signals into G-protein activation and
ultimately into intracellular responses. The mGluRs are
classified into three groups which comprise eight
subtypes.
Length = 463
Score = 25.2 bits (55), Expect = 4.5
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 1 MPKE-ETLEFSGIVSELLPNANFR-VKLITNDDD 32
+P+E EF I+ LL N R V + N+DD
Sbjct: 210 IPREPRPGEFDKIIKRLLETPNARAVIIFANEDD 243
>gnl|CDD|173846 cd01157, MCAD, Medium chain acyl-CoA dehydrogenase. MCADs are
mitochondrial beta-oxidation enzymes, which catalyze the
alpha,beta dehydrogenation of the corresponding medium
chain acyl-CoA by FAD, which becomes reduced. The
reduced form of MCAD is reoxidized in the oxidative
half-reaction by electron-transferring flavoprotein
(ETF), from which the electrons are transferred to the
mitochondrial respiratory chain coupled with ATP
synthesis. MCAD is a homotetramer.
Length = 378
Score = 24.9 bits (54), Expect = 4.6
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 70 VIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTR 102
I + R+ K + I G K+AM +D TR
Sbjct: 209 GITFEDVRVPKENVLIGEGAGFKIAMGAFDKTR 241
>gnl|CDD|143211 cd05734, Ig7_DSCAM, Seventh immunoglobulin (Ig)-like domain of
Down Syndrome Cell Adhesion molecule (DSCAM).
Ig7_DSCAM: the seventh immunoglobulin (Ig)-like domain
of Down Syndrome Cell Adhesion molecule (DSCAM). DSCAM
is a cell adhesion molecule expressed largely in the
developing nervous system. The gene encoding DSCAM is
located at human chromosome 21q22, the locus associated
with the mental retardation phenotype of Down Syndrome.
DSCAM is predicted to be the largest member of the IG
superfamily. It has been demonstrated that DSCAM can
mediate cation-independent homophilic intercellular
adhesion.
Length = 79
Score = 24.5 bits (53), Expect = 7.0
Identities = 10/36 (27%), Positives = 20/36 (55%)
Query: 15 ELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSES 50
+LL N + +K + +D CK+ + V ++ S+S
Sbjct: 39 QLLSNGSLLIKHVLEEDSGYYLCKVSNDVGADASKS 74
>gnl|CDD|36570 KOG1356, KOG1356, KOG1356, Putative transcription factor 5qNCA,
contains JmjC domain [Transcription].
Length = 889
Score = 24.2 bits (52), Expect = 7.5
Identities = 11/63 (17%), Positives = 22/63 (34%), Gaps = 4/63 (6%)
Query: 30 DDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVV----IAYTAGRMRKHRIRI 85
D+S C+ + F++ G + P Y A+ I+ + R+ +
Sbjct: 131 KDESPVFCRFYEFRRLQFTKKGVLRVQGFLSPDQYDPEAISLWGPISGSDSRLDTETAKY 190
Query: 86 SLG 88
L
Sbjct: 191 ILA 193
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.315 0.132 0.365
Gapped
Lambda K H
0.267 0.0768 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,211,932
Number of extensions: 52385
Number of successful extensions: 128
Number of sequences better than 10.0: 1
Number of HSP's gapped: 127
Number of HSP's successfully gapped: 19
Length of query: 110
Length of database: 6,263,737
Length adjustment: 76
Effective length of query: 34
Effective length of database: 4,621,453
Effective search space: 157129402
Effective search space used: 157129402
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 51 (23.3 bits)