RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781056|ref|YP_003065469.1| phage-related lysozyme
[Candidatus Liberibacter asiaticus str. psy62]
(171 letters)
>gnl|CDD|29561 cd00737, endolysin_autolysin, Endolysins and autolysins are found
in viruses and bacteria, respectively. The ds DNA phages
of eubacteria use endolysins or muralytic enzymes in
conjunction with hollin, a small membrane protein, to
degrade the peptidoglycan found in bacterial cell walls.
Similarly, bacteria produce autolysins to facilitate the
biosynthesis of its cell wall hetropolymer peptidoglycan
and cell division. Both endolysin and autolysin enzymes
cleave the glycosidic beta 1,4-bonds between the
N-acetylmuramic acid and the N-acetylglucosamine of the
peptidoglycan..
Length = 133
Score = 135 bits (342), Expect = 5e-33
Identities = 61/137 (44%), Positives = 87/137 (63%), Gaps = 4/137 (2%)
Query: 28 VPNALIKMLKEFEGLRLTAYRDIGGGAWTIGYGHTGSDVTEGMTITEKEAEDFLLKDASK 87
+ A + ++K FEG RLT Y+D G WTIGYGHTG V GMTITE++A+ L KD +K
Sbjct: 1 ISQAGLALIKRFEGCRLTPYKDPAG-VWTIGYGHTGGVV-PGMTITEEQADALLAKDLAK 58
Query: 88 SLNLLLESSPALKSTSENRLVAVADFVFNLGIGNYNKSTFKQRVDAQDWEKAAEECKKWT 147
+ + + ++N+ A+ F FN+G G + ST ++++A DW A + +W
Sbjct: 59 AERAV--NRAVKVPLTQNQFDALVSFAFNVGAGAFRTSTLLRKLNAGDWAGACAQLPRWV 116
Query: 148 KAGGKVLPGLVKRRDAE 164
KAGGKVLPGLV+RR+AE
Sbjct: 117 KAGGKVLPGLVRRREAE 133
>gnl|CDD|33567 COG3772, COG3772, Phage-related lysozyme (muraminidase) [General
function prediction only].
Length = 152
Score = 126 bits (318), Expect = 3e-30
Identities = 59/145 (40%), Positives = 84/145 (57%), Gaps = 2/145 (1%)
Query: 28 VPNALIKMLKEFEGLRLTAYRDIGGGAWTIGYGHTGSDVTEGMTITEKEAEDFLLKDASK 87
+ I ++KEFEG RL YRD G WTIGYGHTG V GMT+T++E + +
Sbjct: 7 ISEIGIALIKEFEGCRLDPYRD-PAGVWTIGYGHTGKPVGPGMTLTKEECDQANALERDL 65
Query: 88 SLNLLLESSPALKSTSENRLVAVADFVFNLGIGNYNKSTFKQRVDAQDWEKAAEECKKWT 147
+ + ++ + A+ F +N+G GN+ ST +R++A DW A E+ ++W
Sbjct: 66 AEAERAVNRYIKVPLTQPQFDALVSFAYNIGAGNFFSSTLLRRINAGDWSGACEQLRRWI 125
Query: 148 KA-GGKVLPGLVKRRDAEVKLLLES 171
KA GGKVLPGLV+RR+AE L L
Sbjct: 126 KAGGGKVLPGLVRRREAERALFLWG 150
>gnl|CDD|144526 pfam00959, Phage_lysozyme, Phage lysozyme. This family includes
lambda phage lysozyme and E. coli endolysin.
Length = 108
Score = 79.7 bits (197), Expect = 4e-16
Identities = 37/111 (33%), Positives = 48/111 (43%), Gaps = 8/111 (7%)
Query: 55 WTIGYGHTGSDVTEGMTITEKEAED---FLLKDASKSLNLLLESSPALKSTSENRLVAVA 111
WTIG GH G+DV+ IT+ A F L A + + S NR A+
Sbjct: 2 WTIGIGHYGTDVSPHPRITKSTAAGRYQFDLDTAERGIKQYG-----KVDFSPNRQDALV 56
Query: 112 DFVFNLGIGNYNKSTFKQRVDAQDWEKAAEECKKWTKAGGKVLPGLVKRRD 162
FN+G G ST + + W A K KAGGK GL +RR+
Sbjct: 57 SLAFNVGCGARGFSTLLRAGNQGQWVLACSAIWKSLKAGGKEYNGLKRRRE 107
>gnl|CDD|29559 cd00735, bacteriophage_T4-like_lysozyme, Bacteriophage T4-like
lysozymes hydrolyse the beta-1,4-glycosidic bond between
N-acetylmuramic acid (MurNAc) and N-acetylglucosamine
(GlcNAc) in peptidoglycan heteropolymers of prokaryotic
cell walls. Members include a variety of bacteriophages
(T4, RB49, RB69, Aeh1) as well as Dictyostelium. .
Length = 164
Score = 45.0 bits (106), Expect = 1e-05
Identities = 41/136 (30%), Positives = 64/136 (47%), Gaps = 26/136 (19%)
Query: 34 KMLKEFEGLRLTAYRDIGGGAWTIGYGH--------------------TGSDVTEGMTIT 73
+ML++ EGLRL Y D G TIG GH G +VT G IT
Sbjct: 4 EMLRQDEGLRLKVYWD-TEGYPTIGIGHLITRKKTKDLNAINSELSKQIGREVTNG-VIT 61
Query: 74 EKEAEDFLLKDASKSLNLLLES---SPALKSTSENRLVAVADFVFNLGIGNYNKSTFKQR 130
+E E KD +K+ ++ + SP K + +R +A+ + VF +G+G K R
Sbjct: 62 SEEVEALFEKDLAKAQRDIMSNPKLSPVYKKLNASRQMALENMVFQMGVGGVAKFKNSLR 121
Query: 131 -VDAQDWEKAAEECKK 145
+ A+DW++A + +
Sbjct: 122 AMAAKDWKEAYKGLRD 137
>gnl|CDD|30089 cd01367, KISc_KIF2_like, Kinesin motor domain, KIF2-like group.
KIF2 is a protein expressed in neurons, which has been
associated with axonal transport and neuron development;
alternative splice forms have been implicated in
lysosomal translocation. This catalytic (head) domain
has ATPase activity and belongs to the larger group of
P-loop NTPases. Kinesins are microtubule-dependent
molecular motors that play important roles in
intracellular transport and in cell division. In this
subgroup the motor domain is found in the middle
(M-type) of the protein chain. M-type kinesins are (+)
end-directed motors, i.e. they transport cargo towards
the (+) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and move
along the microtubule at a speed of about 6400 Angstroms
per second (KIF2 may be slower). To achieve that,
kinesin head groups work in pairs. Upon replacing ADP
with ATP, a kinesin motor domain increases its affinity
for microtubule binding and locks in place. Also, the
neck linker binds to the motor domain, which repositions
the other head domain through the coiled-coil domain
close to a second tubulin dimer, about 80 Angstroms
along the microtubule. Meanwhile, ATP hydrolysis takes
place, and when the second head domain binds to the
microtubule, the first domain again replaces ADP with
ATP, triggering a conformational change that pulls the
first domain forward..
Length = 322
Score = 28.3 bits (63), Expect = 1.0
Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 2/47 (4%)
Query: 51 GGGAWTIGYGHTGSDVTEGMTITEKEAEDFLLKDASKSLNLLLESSP 97
GG A YG TGS T M E + + L A++ + LL
Sbjct: 83 GGVATCFAYGQTGSGKTYTMLGDENQEGLYAL--AARDIFRLLAQPN 127
>gnl|CDD|34745 COG5144, TFB2, RNA polymerase II transcription
initiation/nucleotide excision repair factor TFIIH,
subunit TFB2 [Transcription / DNA replication,
recombination, and repair].
Length = 447
Score = 27.7 bits (61), Expect = 1.7
Identities = 18/63 (28%), Positives = 25/63 (39%), Gaps = 6/63 (9%)
Query: 79 DFLLKDASKSLNLLLESSPALKSTSENRLVAVADFVFNLG---IGNYNKSTF---KQRVD 132
FLL+ ++ L LL S VAV F+F LG +G K Q++
Sbjct: 184 QFLLQTINEQLWTLLLLYLKYFEGSVMDEVAVLHFLFMLGALAVGTAYKIDALSDTQQIM 243
Query: 133 AQD 135
D
Sbjct: 244 LMD 246
>gnl|CDD|35655 KOG0434, KOG0434, KOG0434, Isoleucyl-tRNA synthetase [Translation,
ribosomal structure and biogenesis].
Length = 1070
Score = 26.8 bits (59), Expect = 2.7
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 112 DFVFNLGIGNYNKSTFKQRVD-AQDWEKAAEECKKW 146
D V +GI YN K + + +WEK E +W
Sbjct: 105 DDVMKMGIDKYNNECRKIVMRYSSEWEKTVERLGRW 140
>gnl|CDD|153385 cd07373, 2A5CPDO_A, The alpha subunit of the Class III extradiol
dioxygenase, 2-amino-5-chlorophenol 1,6-dioxygenase,
which catalyzes the oxidization and subsequent
ring-opening of 2-amino-5-chlorophenol.
2-amino-5-chlorophenol 1,6-dioxygenase (2A5CPDO)
catalyzes the oxidization and subsequent ring-opening of
2-amino-5-chlorophenol, which is an intermediate during
p-chloronitrobenzene degradation. This enzyme is a
member of the class III extradiol dioxygenase family, a
group of enzymes which use a non-heme Fe(II) to cleave
aromatic rings between a hydroxylated carbon and an
adjacent non-hydroxylated carbon. The active enzyme is
probably a heterotetramer, composed of two alpha and two
beta subunits. The alpha and beta subunits share
significant sequence similarity and may have evolved by
gene duplication. This model describes the alpha
subunit, which does not contain a potential metal
binding site and may not possess catalytic activity.
Length = 271
Score = 26.8 bits (59), Expect = 3.0
Identities = 14/45 (31%), Positives = 25/45 (55%), Gaps = 6/45 (13%)
Query: 104 ENRLVAVADFVFNLGIGNYNKSTFKQRVDAQDWEKAAEECKKWTK 148
+N+ VAV +G+G + S F++ +D ++ A EE KW +
Sbjct: 165 QNKRVAV------VGVGGLSGSLFREEIDPREDHIANEEDDKWNR 203
>gnl|CDD|32176 COG1993, COG1993, Uncharacterized conserved protein [Function
unknown].
Length = 109
Score = 26.7 bits (59), Expect = 3.1
Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 8/59 (13%)
Query: 6 RIISFVKRMIGMNGDDKHNKIPVPNALIKMLKEFEGLR-LTAYRDIGGGAWTIGYGHTG 63
+ + I + +DKH P+ A+++ L+E EG+R T R I G+G G
Sbjct: 2 KRMKSKLLRIYLGENDKHEGKPLYEAIVERLRE-EGIRGATVLRGI------AGFGKDG 53
>gnl|CDD|35767 KOG0547, KOG0547, KOG0547, Translocase of outer mitochondrial
membrane complex, subunit TOM70/TOM72 [Intracellular
trafficking, secretion, and vesicular transport].
Length = 606
Score = 26.5 bits (58), Expect = 3.8
Identities = 14/65 (21%), Positives = 20/65 (30%), Gaps = 6/65 (9%)
Query: 108 VAVADFVFNLGIGNYNKSTFKQRVDAQD------WEKAAEECKKWTKAGGKVLPGLVKRR 161
VA G + + A E A ++ K GK + G KR
Sbjct: 20 TVVAGGTAVGGYYYLQQWQLALQDGAPLKIGEGKNEAAKVVKEEDLKDSGKDVEGAKKRA 79
Query: 162 DAEVK 166
A+ K
Sbjct: 80 KAKNK 84
>gnl|CDD|35718 KOG0497, KOG0497, KOG0497, Oxidosqualene-lanosterol cyclase and
related proteins [Lipid transport and metabolism].
Length = 760
Score = 26.4 bits (58), Expect = 4.2
Identities = 22/93 (23%), Positives = 34/93 (36%), Gaps = 17/93 (18%)
Query: 47 YRDIGGGAWTIGYGHTGSDVTEGMTITEKEAEDFLLKDASKSLNLLLESSPA---LKSTS 103
YR I G WT SD +G +++ AE + LLL S P+ +
Sbjct: 464 YRHISKGGWTF------SDRDQGWPVSDCTAE-------ALKCCLLLSSMPSEIVGEKID 510
Query: 104 ENRLVAVADFVFNLGIGNYNKSTFKQRVDAQDW 136
RL D + L N + + + +W
Sbjct: 511 VERLYDAVDVLLYLQSENGGFAAY-EPARGYEW 542
>gnl|CDD|58126 cd03721, SOCS_ASB2, SOCS (suppressors of cytokine signaling) box
of ASB2-like proteins. ASB family members have a
C-terminal SOCS box and an N-terminal ankyrin-related
sequence. ASB2 targets specific proteins to destruction
by the proteasome in leukemia cells that have been
induced to differentiate. The general function of the
SOCS box is the recruitment of the
ubiquitin-transferase system. The SOCS box interacts
with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and
E2. Therefore, SOCS-box-containing proteins probably
function as E3 ubiquitin ligases and mediate the
degradation of proteins associated through their
N-terminal regions..
Length = 45
Score = 26.4 bits (58), Expect = 4.4
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 11 VKRMIGMNGDDKHNKIPVPNALIKMLK 37
V+ +IG+N + +P+P LI+ L
Sbjct: 14 VRTLIGINRIKLIDTLPLPPRLIRYLN 40
>gnl|CDD|35483 KOG0262, KOG0262, KOG0262, RNA polymerase I, large subunit
[Transcription].
Length = 1640
Score = 26.1 bits (57), Expect = 5.2
Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 8/74 (10%)
Query: 35 MLKEFEGLRL---TAYRDIGGGAWTIGYGHTGSDVTEGMTITEKE-----AEDFLLKDAS 86
++K EGL++ RD G YG G D+T+ + +KE E LLK S
Sbjct: 995 LIKHLEGLKVHYDLTVRDSDGSVVQFMYGEDGLDITKSSFLNKKEFPTDNYEAVLLKYKS 1054
Query: 87 KSLNLLLESSPALK 100
+S+ + A K
Sbjct: 1055 ESVLSAFDIKKASK 1068
>gnl|CDD|37107 KOG1896, KOG1896, KOG1896, mRNA cleavage and polyadenylation factor
II complex, subunit CFT1 (CPSF subunit) [RNA processing
and modification].
Length = 1366
Score = 26.1 bits (57), Expect = 5.6
Identities = 12/40 (30%), Positives = 23/40 (57%)
Query: 80 FLLKDASKSLNLLLESSPALKSTSENRLVAVADFVFNLGI 119
FL+ DA +++++ + + ++S S RLV ADF +
Sbjct: 1198 FLVSDADRNIHVYMYAPENIESLSGQRLVRRADFHVGAHV 1237
>gnl|CDD|29558 cd00442, lysozyme_like, lysozyme_like domain. This contains
several members including Soluble Lytic
Transglycosylases (SLT), Goose Egg-White Lysozymes
(GEWL), Hen Egg-White Lysozymes (HEWL), chitinases,
bacteriophage lambda lysozymes, endolysins, autolysins,
and chitosanases. All the members are involved in the
hydrolysis of beta-1,4- linked polysaccharides..
Length = 105
Score = 25.4 bits (55), Expect = 8.0
Identities = 21/70 (30%), Positives = 27/70 (38%), Gaps = 10/70 (14%)
Query: 31 ALIKMLKEFEGLRLTAYRDIGG-------GAWTIG-YGHT--GSDVTEGMTITEKEAEDF 80
A+I ML EG L AY+D G + IG Y T SD I K
Sbjct: 1 AIIDMLASSEGTDLKAYKDRGHGTLNPGERGYGIGLYQLTSRWSDAYRARGIGLKLLAQL 60
Query: 81 LLKDASKSLN 90
+LK + +
Sbjct: 61 ILKLFNPKVQ 70
>gnl|CDD|36002 KOG0783, KOG0783, KOG0783, Uncharacterized conserved protein,
contains ankyrin and BTB/POZ domains [Function unknown].
Length = 1267
Score = 25.4 bits (55), Expect = 8.7
Identities = 13/54 (24%), Positives = 19/54 (35%), Gaps = 4/54 (7%)
Query: 83 KDASKSLNLLLESSPA---LKSTSENRLVAVADFV-FNLGIGNYNKSTFKQRVD 132
K+ L L + N + V LGIGN + + +RVD
Sbjct: 117 KEGLSPLQFLSRVLSSTIHPVLDLPNDVYGWGTNVNNTLGIGNGKEPSSPERVD 170
>gnl|CDD|35265 KOG0042, KOG0042, KOG0042, Glycerol-3-phosphate dehydrogenase
[Energy production and conversion].
Length = 680
Score = 25.3 bits (55), Expect = 9.1
Identities = 17/43 (39%), Positives = 20/43 (46%), Gaps = 2/43 (4%)
Query: 50 IGGGAWTIGYGHTGSDVTEGMTITEKEAEDFLLKDASKSLNLL 92
IGGGA G G T G+ EA DF +SKS L+
Sbjct: 73 IGGGA--TGAGCALDAATRGLKTALVEAGDFASGTSSKSTKLI 113
>gnl|CDD|143580 cd07176, terB, tellurite resistance protein terB. This family
contains uncharacterized bacterial proteins involved in
tellurium resistance. The prototype of this CD is the
Kp-terB protein from Klebsiella pneumoniae, whose 3D
structure was recently determined. The biological
function of terB and the mechanism responsible for
tellurium resistance are unknown.
Length = 111
Score = 25.3 bits (56), Expect = 9.8
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 92 LLESSPALKSTSENRLVAVADFVFNL 117
LL S P L RL+A+ D + L
Sbjct: 30 LLRSLPVLSGFDRERLIALLDKLLAL 55
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
0.316 0.135 0.389
Gapped
Lambda K H
0.267 0.0701 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,998,069
Number of extensions: 96009
Number of successful extensions: 234
Number of sequences better than 10.0: 1
Number of HSP's gapped: 226
Number of HSP's successfully gapped: 21
Length of query: 171
Length of database: 6,263,737
Length adjustment: 87
Effective length of query: 84
Effective length of database: 4,383,754
Effective search space: 368235336
Effective search space used: 368235336
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 (21.6 bits)
S2: 54 (24.6 bits)