RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2880
(166 letters)
>gnl|CDD|234668 PRK00150, def, peptide deformylase; Reviewed.
Length = 165
Score = 225 bits (577), Expect = 7e-77
Identities = 80/163 (49%), Positives = 114/163 (69%), Gaps = 1/163 (0%)
Query: 1 MTLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLI 60
M +LPI+ Y D L+K+A+P+ E D L+K+I +M ETMY A G+GLAA QV + K++++
Sbjct: 1 MAILPILRYGDPVLRKVAKPVEEVDDELRKLIDDMFETMYAAPGVGLAAPQVGVSKRIIV 60
Query: 61 LDISKNNNQLQVFINPKIIWYSK-EKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKM 119
+D+ + V INP+II S E Y EGCLS+PG++ ++ R +R+ V AL+ +GK
Sbjct: 61 IDVEDKEGEPLVLINPEIISESSEEYLTYEEGCLSVPGVYGEVPRPERVTVKALDRDGKP 120
Query: 120 FEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLK 162
FE+ A+GLLA C+QHEIDHLNG +FI+ LS K+ RI KK K
Sbjct: 121 FELEADGLLARCIQHEIDHLNGVLFIDRLSPLKRFRIKKKLKK 163
>gnl|CDD|237227 PRK12846, PRK12846, peptide deformylase; Reviewed.
Length = 165
Score = 213 bits (544), Expect = 8e-72
Identities = 72/163 (44%), Positives = 108/163 (66%), Gaps = 1/163 (0%)
Query: 1 MTLLPIIYYPDIRLKKIAEPITEFDIN-LKKIIFNMTETMYHAMGIGLAASQVDIHKQLL 59
M + PI+ PD RL++ AEP+T FD L+ +I +M ETM A G+GLAA Q+ + +++
Sbjct: 1 MAVRPILKMPDPRLRRPAEPVTAFDTEELQALIDDMFETMRAADGVGLAAPQIGVSLRVV 60
Query: 60 ILDISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKM 119
++D+ + V INP+I S E+++ EGCLS+PG+ +++R R+RV A + +GK
Sbjct: 61 VIDLGDDRVPPTVLINPEITELSPEEEVGWEGCLSVPGLRGEVERPARVRVRAQDRDGKP 120
Query: 120 FEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLK 162
EI AEG LA LQHEIDHL+G ++ + LS K+ER +KK K
Sbjct: 121 IEIEAEGFLARVLQHEIDHLDGILYTDRLSRLKRERALKKVEK 163
>gnl|CDD|223320 COG0242, Def, N-formylmethionyl-tRNA deformylase [Translation,
ribosomal structure and biogenesis].
Length = 168
Score = 210 bits (537), Expect = 1e-70
Identities = 77/168 (45%), Positives = 114/168 (67%), Gaps = 3/168 (1%)
Query: 1 MTLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLI 60
M + I+ YPD RL+++A+P+ E D L+++I +M ETMY A G+GLAA Q+ I K++ +
Sbjct: 1 MAIREIVKYPDPRLRQVAKPVEEVDDELRQLIDDMLETMYAAEGVGLAAPQIGISKRIFV 60
Query: 61 LDISKNNNQLQ---VFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEG 117
+D+ ++ + V INP+II S+E EGCLS+PG+ +++R +RI V L+ G
Sbjct: 61 IDVEEDGRPKEPPLVLINPEIISKSEETLTGEEGCLSVPGVRGEVERPERITVKYLDRNG 120
Query: 118 KMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLKNIK 165
K E+ AEGLLA C+QHEIDHLNG +FI+ LS K++R+ KK K K
Sbjct: 121 KPQELEAEGLLARCIQHEIDHLNGVLFIDRLSPLKRDRLKKKLKKLKK 168
>gnl|CDD|216435 pfam01327, Pep_deformylase, Polypeptide deformylase.
Length = 155
Score = 190 bits (485), Expect = 4e-63
Identities = 69/154 (44%), Positives = 102/154 (66%), Gaps = 3/154 (1%)
Query: 4 LPIIYYPDIRLKKIAEPITEFDIN-LKKIIFNMTETMYHAMGIGLAASQVDIHKQLLILD 62
LPI+ YPD L++ A+P+ EFD LK++I +M ETMY A G+GLAA Q+ + K++ ++D
Sbjct: 2 LPIVTYPDPVLRQKAKPVEEFDDEELKELIDDMLETMYAANGVGLAAPQIGVSKRIFVID 61
Query: 63 ISKNNNQ--LQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMF 120
+ + + V INP+II S+E EGCLS+PG+ +++R KRI V ++ G
Sbjct: 62 VGDEDGEPEPLVLINPEIISASEETVEGEEGCLSVPGLRGEVERPKRITVRYQDLNGNEH 121
Query: 121 EIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKE 154
E+ A+G LA LQHEIDHLNG +F++ LS K+
Sbjct: 122 ELEADGFLARVLQHEIDHLNGILFLDRLSKLKRL 155
>gnl|CDD|238271 cd00487, Pep_deformylase, Polypeptide or peptide deformylase; a
family of metalloenzymes that catalyzes the removal of
the N-terminal formyl group in a growing polypeptide
chain following translation initiation during protein
synthesis in prokaryotes. These enzymes utilize Fe(II)
as the catalytic metal ion, which can be replaced with a
nickel or cobalt ion with no loss of activity. There are
two types of peptide deformylases, types I and II, which
differ in structure only in the outer surface of the
domain. Because these enzymes are essential only in
prokaryotes (although eukaryotic gene sequences have
been found), they are a target for a new class of
antibacterial agents.
Length = 141
Score = 189 bits (483), Expect = 6e-63
Identities = 66/141 (46%), Positives = 95/141 (67%), Gaps = 2/141 (1%)
Query: 6 IIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLILDISK 65
I+ YPD L+K A+P+ EFD LK++I +M ETMY A G+GLAA Q+ + K++ ++D+
Sbjct: 1 IVQYPDPVLRKKAKPVEEFDDELKQLIDDMFETMYAAPGVGLAAPQIGVSKRIFVIDVPD 60
Query: 66 NNNQLQ--VFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFEII 123
N+ V INP+II S E + EGCLS+PG +++R K++ V L+ +G E+
Sbjct: 61 EENKEPPLVLINPEIIESSGETEYGEEGCLSVPGYRGEVERPKKVTVRYLDEDGNPIELE 120
Query: 124 AEGLLAICLQHEIDHLNGKIF 144
AEG LA C+QHEIDHLNG +F
Sbjct: 121 AEGFLARCIQHEIDHLNGILF 141
>gnl|CDD|237761 PRK14597, PRK14597, peptide deformylase; Provisional.
Length = 166
Score = 143 bits (362), Expect = 3e-44
Identities = 70/161 (43%), Positives = 100/161 (62%), Gaps = 3/161 (1%)
Query: 6 IIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLILDISK 65
I + D L+K A+P+T+FD NLKK I M ETMYH G+GLAA QV I + ++D
Sbjct: 3 IRLFGDPVLRKKAKPVTKFDDNLKKTIEEMIETMYHYDGVGLAAPQVGISLRFFVMD--- 59
Query: 66 NNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFEIIAE 125
+ + +V INP+II S+EK+I EGCLS P IF ++RSK ++V + G++ E + E
Sbjct: 60 DGSGPKVVINPEIIEKSEEKEIAEEGCLSFPEIFEDVERSKWVKVRYQDERGEVVEELLE 119
Query: 126 GLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLKNIKK 166
G A QHE DHLNG +FI+ L K+ + KK + ++
Sbjct: 120 GYAARIFQHEYDHLNGVLFIDRLPPAKRLLLRKKLMDIMRT 160
>gnl|CDD|232815 TIGR00079, pept_deformyl, peptide deformylase. Peptide deformylase
(EC 3.5.1.88), also called polypeptide deformylase, is a
metalloenzyme that uses water to release formate from
the N-terminal formyl-L-methionine of bacterial and
chloroplast peptides. This enzyme should not be confused
with formylmethionine deformylase (EC 3.5.1.31) which is
active on free N-formyl methionine and has been reported
from rat intestine [Protein fate, Protein modification
and repair].
Length = 161
Score = 134 bits (339), Expect = 8e-41
Identities = 61/158 (38%), Positives = 101/158 (63%), Gaps = 1/158 (0%)
Query: 3 LLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLILD 62
+L + +YPD L+K A+P+ D + + + +M ETM GIGLAA QV I K++++++
Sbjct: 1 MLEVFHYPDDLLRKTAKPVEIVDKKIDQQLDDMIETMIAEKGIGLAAPQVGILKRMIVIE 60
Query: 63 ISKNNNQLQVF-INPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFE 121
+ + + +F INPKII S+E EGCLS+P + + R +++++ + GK
Sbjct: 61 LEDADKEPLLFLINPKIIESSEESSYLEEGCLSVPVYYGLVPRKEKVKIRGDDRFGKPII 120
Query: 122 IIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKK 159
+ A+GLLAIC+QHEIDHLNG F++Y+S +++ K+
Sbjct: 121 LEADGLLAICIQHEIDHLNGVFFVDYISPLNPKKLKKE 158
>gnl|CDD|184758 PRK14596, PRK14596, peptide deformylase; Provisional.
Length = 199
Score = 127 bits (320), Expect = 1e-37
Identities = 57/172 (33%), Positives = 95/172 (55%), Gaps = 17/172 (9%)
Query: 3 LLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLI-- 60
+ PI Y D L++ A P+ +FD ++++ +M ETM+ A G+GLAA Q+ + +L +
Sbjct: 2 VYPIRLYGDPVLRRKARPVQDFDQGIRRLAEDMLETMFEARGVGLAAPQIGLSVRLFVAV 61
Query: 61 --LDISKNNN-----------QLQVFINPKIIWYSKEKQIYNEGCLSLPGIF-NKIKRSK 106
D + + V +NP I Y K Q EGCLS+PG++ + R++
Sbjct: 62 EYADDEEEEEGEEAPLRSRVLREYVMVNPVIT-YRKGDQSGQEGCLSIPGLYEEGVPRAR 120
Query: 107 RIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIK 158
++RV +++G+ + AEG LA QHEIDHL+G +F + L K+E ++
Sbjct: 121 QVRVEYQDLDGQKRTLEAEGYLARVFQHEIDHLDGILFFDRLPKAKREAFLE 172
>gnl|CDD|237762 PRK14598, PRK14598, peptide deformylase; Provisional.
Length = 187
Score = 112 bits (282), Expect = 7e-32
Identities = 61/170 (35%), Positives = 94/170 (55%), Gaps = 10/170 (5%)
Query: 3 LLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLILD 62
+LPI Y D L++ A+P+ D ++++I +M E+MY+A GIGLAA QV +LL++D
Sbjct: 2 ILPINTYSDEVLRQKAKPLKGVDAEIEELIASMFESMYNASGIGLAAPQVGRSLRLLVVD 61
Query: 63 IS----KNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGK 118
+S + + V INP I+ K EGCLS+PG+ + R I + +
Sbjct: 62 VSCMKEYEDEKPMVVINPHIL-AVKGYNAMEEGCLSVPGVQGDVVRPSSITLKYRD--EH 118
Query: 119 MFEIIAE--GLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLKNIKK 166
E E G++A LQHEIDHL+G +F++ + + R I+K L I
Sbjct: 119 FEERTEEFSGMMARVLQHEIDHLDGTLFVDRMQK-RDRRKIQKELDAIAA 167
>gnl|CDD|184757 PRK14595, PRK14595, peptide deformylase; Provisional.
Length = 162
Score = 98.0 bits (244), Expect = 2e-26
Identities = 46/163 (28%), Positives = 81/163 (49%), Gaps = 2/163 (1%)
Query: 1 MTLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLI 60
M + ++ L K A+ + FD +LK+++ ++ +TMY L A Q+ Q+ I
Sbjct: 1 MAIKKLVPASHPILTKKAQAVKTFDDSLKRLLQDLEDTMYAQEAAALCAPQIGQSLQVAI 60
Query: 61 LDISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMF 120
+D+ L +NPKII S E EG ++LP ++ ++ RSK I V + ++ G
Sbjct: 61 IDMEMEG--LLQLVNPKIISQSNETITDLEGSITLPDVYGEVTRSKMIVVESYDVNGNKV 118
Query: 121 EIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLKN 163
E+ A +A + H ID +NG F E ++ ++ + N
Sbjct: 119 ELTAYDDVARMILHIIDQMNGIPFTERADRILTDKEVEAYFIN 161
>gnl|CDD|181704 PRK09218, PRK09218, peptide deformylase; Validated.
Length = 136
Score = 62.6 bits (153), Expect = 3e-13
Identities = 30/99 (30%), Positives = 47/99 (47%), Gaps = 5/99 (5%)
Query: 45 IGLAASQVDIHKQLLILDISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKR 104
+G+AA+ + + K+++I + V NP I+ S + EGCLSL G KR
Sbjct: 42 VGMAANMIGVQKRIIIFSLGFVP---VVMFNPVIVSKSGPYETE-EGCLSLTG-ERPTKR 96
Query: 105 SKRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKI 143
+ I V L+ + G A +QHE+DH G +
Sbjct: 97 YEEITVKYLDRNWREQTQTFTGFTAQIIQHELDHCEGIL 135
>gnl|CDD|188706 cd08752, RGS_GRK5, Regulator of G protein signaling domain (RGS)
found in G protein-coupled receptor kinase 5 (GRK5).
The RGS domain is an essential part of the GRK5 (G
protein-coupled receptor kinase 5) protein, a
membrane-associated serine/threonine protein kinases
which phosphorylates G protein-coupled receptors (GPCRs)
upon agonist stimulation. This phosphorylation initiates
beta-arrestin-mediated receptor desensitization,
internalization, and signaling events. GRK5 is a member
of the GRK kinase family which include three major
subfamilies: the GRK4 subfamily (GRK4, GRK5 and GRK6),
the rhodopsin kinase or visual GRK subfamily (GRK1 and
GRK7), and the beta-adrenergic receptor kinases
subfamily (GRK2/GRK3). The RGS domain of the GRKs has
very little sequence similarity with the canonical RGS
domain of the RGS proteins and therefore is often
refered to as the RH (RGS Homology) domain. RGS proteins
regulate many aspects of embryonic development such as
glial differentiation, embryonic axis formation,
skeletal and muscle development, cell migration during
early embryogenesis, as well as apoptosis, cell
proliferation, and modulation of cardiac development.
Length = 123
Score = 27.3 bits (60), Expect = 2.2
Identities = 13/43 (30%), Positives = 23/43 (53%)
Query: 116 EGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIK 158
E K+ + + L + C Q D+L G+ F EYL + +R ++
Sbjct: 78 EEKLLQKPCKELFSACTQSVHDYLRGEPFHEYLDSMYFDRFLQ 120
>gnl|CDD|211576 TIGR00459, aspS_bact, aspartyl-tRNA synthetase, bacterial type.
Asparate--tRNA ligases in this family may be
discriminating (6.1.1.12) or nondiscriminating
(6.1.1.23). In a multiple sequence alignment of
representative asparaginyl-tRNA synthetases (asnS),
archaeal/eukaryotic type aspartyl-tRNA synthetases
(aspS_arch), and bacterial type aspartyl-tRNA
synthetases (aspS_bact), there is a striking similarity
between asnS and aspS_arch in gap pattern and in
sequence, and a striking divergence of aspS_bact.
Consequently, a separate model was built for each of the
three groups. This model, aspS_bact, represents
aspartyl-tRNA synthetases from the Bacteria and from
mitochondria. In some species, this enzyme aminoacylates
tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently
transamidated to Asn-tRNA(asn). This model generates
very low scores for the archaeal type of aspS and for
asnS; scores between the trusted and noise cutoffs
represent fragmentary sequences [Protein synthesis, tRNA
aminoacylation].
Length = 583
Score = 28.2 bits (63), Expect = 2.3
Identities = 14/73 (19%), Positives = 29/73 (39%), Gaps = 4/73 (5%)
Query: 55 HKQLLILDISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALN 114
L+ +D+ + +QV +P K + NE + + G ++ N
Sbjct: 30 LGGLIFIDLRDRSGIVQVVCDPDADALKLAKGLRNEDVVQVKGKV----SARPEGNINRN 85
Query: 115 IEGKMFEIIAEGL 127
++ EI+AE +
Sbjct: 86 LDTGEIEILAESI 98
>gnl|CDD|129359 TIGR00257, IMPACT_YIGZ, uncharacterized protein, YigZ family. This
uncharacterized protein family includes YigZ, which has
been crystallized, from E. coli. YigZ is homologous to
the protein product of the mouse IMPACT gene.
Crystallography shows a two-domain stucture, and the
C-terminal domain is suggested to bind nucleic acids.
The function is unknown. Note that the ortholog from E.
coli was shown fused to the pepQ gene in GenBank entry
X54687. This caused occasional misidentification of this
protein as pepQ; this family is found in a number of
species that lack pepQ [Unknown function, General].
Length = 204
Score = 27.5 bits (61), Expect = 3.4
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 143 IFIEYLSNFKKERIIKKFLKNIKK 166
FI YL++ + KKF++ IKK
Sbjct: 21 RFITYLAHTEGVDDAKKFIEKIKK 44
>gnl|CDD|129815 TIGR00732, dprA, DNA protecting protein DprA. Disruption of this
gene in both Haemophilus influenzae and Helicobacter
pylori drastically reduces the efficiency of
transformation with exogenous DNA, but with different
levels of effect on chromosomal (linear) and plasmid
(circular) DNA. This difference suggests the DprA is not
active in recombination, and it has been shown not to
affect DNA binding, leaving the intermediate step in
natural transformation, DNA processing. In Strep.
pneumoniae, inactivation of dprA had no effect on the
uptake of DNA. All of these data indicated that DprA is
required at a later stage in transformation.
Subsequently DprA and RecA were both shown in S.
pneumoniae to be required to protect incoming ssDNA from
immediate degradation. Role of DprA in non-transformable
species is not known. The gene symbol smf was assigned
in E. coli, but without assignment of function [Cellular
processes, DNA transformation].
Length = 220
Score = 26.9 bits (60), Expect = 5.5
Identities = 12/50 (24%), Positives = 20/50 (40%), Gaps = 6/50 (12%)
Query: 112 ALNIEGKMFEIIAEGLLAI------CLQHEIDHLNGKIFIEYLSNFKKER 155
AL + G+ ++ GL I L +I G + EY + K +
Sbjct: 93 ALKVNGRTIAVLGTGLDQIYPRQNSKLAAKIAENGGLLLSEYPPDTKPIK 142
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
0.325 0.143 0.410
Gapped
Lambda K H
0.267 0.0715 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,833,749
Number of extensions: 836337
Number of successful extensions: 1164
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1147
Number of HSP's successfully gapped: 42
Length of query: 166
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 76
Effective length of database: 6,945,742
Effective search space: 527876392
Effective search space used: 527876392
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: 55 (25.0 bits)