RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7929
(259 letters)
>gnl|CDD|221887 pfam12998, ING, Inhibitor of growth proteins N-terminal
histone-binding. Histones undergo numerous
post-translational modifications, including acetylation
and methylation, at residues which are then probable
docking sites for various chromatin remodelling
complexes. Inhibitor of growth proteins (INGs)
specifically bind to residues that have been thus
modified. INGs carry a well-characterized C-terminal
PHD-type zinc-finger domain, binding with lysine
4-tri-methylated histone H3 (H3K4me3), as well as this
N-terminal domain that binds unmodified H3 tails.
Although these two regions can bind histones
independently, together they increase the apparent
association of the ING for the H3 tail.
Length = 104
Score = 136 bits (344), Expect = 7e-41
Identities = 48/104 (46%), Positives = 71/104 (68%), Gaps = 1/104 (0%)
Query: 4 SYLEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMK-HYSKDKKKE 62
YLE YLD L++LP+ELQRNFT +RE+D++ Q ++K +D + ++ + S K++E
Sbjct: 1 LYLEDYLDDLENLPLELQRNFTEIREIDAQVQKIIKELDEQIQKFIKENGSNLSNPKEEE 60
Query: 63 TLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARF 106
L IQ+ K +E D+KVQLA Q YE+VDK+IR+LD DL +
Sbjct: 61 LLKRIQEELIKAQELQDEKVQLANQAYELVDKHIRRLDKDLEKL 104
>gnl|CDD|227367 COG5034, TNG2, Chromatin remodeling protein, contains PhD zinc
finger [Chromatin structure and dynamics].
Length = 271
Score = 131 bits (331), Expect = 4e-37
Identities = 69/274 (25%), Positives = 100/274 (36%), Gaps = 25/274 (9%)
Query: 1 MSTSY-LEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMK------TIDRVAEDYLDNMK 53
L D L ++P E FT + E+D++ D++K +I + D
Sbjct: 1 ADLFPGLNDITDHLANVPSETDIRFTELSEIDAKVCDIIKNLRQMISILKKIIDLDSQTY 60
Query: 54 HYSKDKKKETLAEI-QKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLAR-----FE 107
+D + + E+ K KE K LA + +++ ++ + LD +A+
Sbjct: 61 EEVEDGLLKEIRELLLKAIYIQKE----KSDLADRAEKLLRRHRKLLDDRIAKRPHEKVA 116
Query: 108 QEIQEKALKNTTGGAGGGGSGTGSGSGSAGGAASKSKRGRKKAKDKAESATDAAGDDKSS 167
I+ + S SG AAS K K + +S
Sbjct: 117 ARIENCHDAVSRLERNSYSSAARRSSGEHRSAASSQGSRHTKLKKRKNIHN---LKRRSP 173
Query: 168 NSKKKVAKKITGVGGVVGVLNAIVA---ADPDVAAPSHDVLDMPVDPNEPTYCVCQQVSY 224
K T V V + D E YC CQQVSY
Sbjct: 174 ELSSKREVSFTLESPSVPDTATRVKEGNNGGSTKSRGVSSEDNSEG--EELYCFCQQVSY 231
Query: 225 GEMIGCDNPDCPIEWFHFACVSLTTKPKGKWYCP 258
G+M+ CDN +C EWFH CV L PKGKWYCP
Sbjct: 232 GQMVACDNANCKREWFHLECVGLKEPPKGKWYCP 265
>gnl|CDD|201356 pfam00628, PHD, PHD-finger. PHD folds into an interleaved type of
Zn-finger chelating 2 Zn ions in a similar manner to
that of the RING and FYVE domains. Several PHD fingers
have been identified as binding modules of methylated
histone H3.
Length = 51
Score = 52.9 bits (127), Expect = 9e-10
Identities = 21/50 (42%), Positives = 28/50 (56%), Gaps = 9/50 (18%)
Query: 216 YC-VCQQV-SYGEMIGCDNPDCPIEWFHFACVSLT----TKPKGKWYCPK 259
YC VC +V GE++ CD C WFH AC+ P+G+WYCP+
Sbjct: 1 YCAVCGKVDDDGELLLCDG--CD-RWFHLACLGPPLEPEEIPEGEWYCPE 47
>gnl|CDD|214584 smart00249, PHD, PHD zinc finger. The plant homeodomain (PHD)
finger is a C4HC3 zinc-finger-like motif found in
nuclear proteins thought to be involved in epigenetics
and chromatin-mediated transcriptional regulation. The
PHD finger binds two zinc ions using the so-called
'cross-brace' motif and is thus structurally related to
the RING finger and the FYVE finger. It is not yet known
if PHD fingers have a common molecular function. Several
reports suggest that it can function as a
protein-protein interacton domain and it was recently
demonstrated that the PHD finger of p300 can cooperate
with the adjacent BROMO domain in nucleosome binding in
vitro. Other reports suggesting that the PHD finger is a
ubiquitin ligase have been refuted as these domains were
RING fingers misidentified as PHD fingers.
Length = 47
Score = 47.2 bits (112), Expect = 9e-08
Identities = 20/49 (40%), Positives = 25/49 (51%), Gaps = 8/49 (16%)
Query: 216 YC-VCQQV-SYGEMIGCDNPDCPIEWFHFACVSLTTK---PKGKWYCPK 259
YC VC + GE++ CD C W+H C+ P GKWYCPK
Sbjct: 1 YCSVCGKPDDGGELLQCDG--CD-RWYHQTCLGPPLLEEEPDGKWYCPK 46
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 37.6 bits (87), Expect = 0.006
Identities = 23/87 (26%), Positives = 33/87 (37%), Gaps = 3/87 (3%)
Query: 102 DLARFEQEIQEKALKNTTGGAGGGGSGTGSGSGSAGG---AASKSKRGRKKAKDKAESAT 158
+ R +E + + GG G G G+ SGS GG A + R + K + E
Sbjct: 416 TIFREAREQRAAEEQRRGGGRSGPGGGSRSGSVGGGGRRDGAGADGKPRPRRKPRVEGEA 475
Query: 159 DAAGDDKSSNSKKKVAKKITGVGGVVG 185
DAA + A + GV G
Sbjct: 476 DAAAAGAETPVVAAAAAQAPGVVAADG 502
>gnl|CDD|233430 TIGR01477, RIFIN, variant surface antigen, rifin family. This
model represents the rifin branch of the rifin/stevor
family (pfam02009) of predicted variant surface antigens
as found in Plasmodium falciparum. This model is based
on a set of rifin sequences kindly provided by Matt
Berriman from the Sanger Center. This is a global model
and assesses a penalty for incomplete sequence.
Additional fragmentary sequences may be found with the
fragment model and a cutoff of 20 bits.
Length = 353
Score = 35.9 bits (83), Expect = 0.014
Identities = 44/170 (25%), Positives = 68/170 (40%), Gaps = 14/170 (8%)
Query: 31 DSRAQDVMKTIDRVA----EDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKV--QL 84
D + VM+ DR E+Y + M+ + K++ EIQK K DK+ +L
Sbjct: 57 DPEMKSVMEQFDRQTSQRFEEYDERMQEKRQKCKEQCDKEIQKIILK------DKLEKEL 110
Query: 85 AIQTYEMVDKYIRKLDTDLARFEQEIQEKALKNTTGGAGGGGSGTGSGSGSAGGAASKSK 144
+ + + I+ E+ + +K K G G G G G GG A
Sbjct: 111 TEK-FSTLQTDIQTDAIPTCVCEKSLADKVEKGCLRCGCGLGGGVAPGVGLLGGIAVNVV 169
Query: 145 RGRKKAKDKAESATDAAGDDKSSNSKKKVAKKITGVGGVVGV-LNAIVAA 193
++ A A +A AAG N + KKI G+ + G L I+ A
Sbjct: 170 GWKQAALAAAAAAAIAAGIKAGINVVIEGLKKILGLSTLFGKKLKQIINA 219
>gnl|CDD|233261 TIGR01073, pcrA, ATP-dependent DNA helicase PcrA. Designed to
identify pcrA members of the uvrD/rep subfamily [DNA
metabolism, DNA replication, recombination, and repair].
Length = 726
Score = 35.5 bits (82), Expect = 0.023
Identities = 25/98 (25%), Positives = 36/98 (36%), Gaps = 11/98 (11%)
Query: 104 ARFEQEIQEKALKNTTGGAGGGGSGTGSGSGSAGGAASKSKRGRKKAKDKAESATDAAGD 163
+RF EI + L+ + G G + S + G + S A GD
Sbjct: 626 SRFLNEIPAELLETASTGRRTGATDPK--------GPSIRQAGASR---PTTSQPTAGGD 674
Query: 164 DKSSNSKKKVAKKITGVGGVVGVLNAIVAADPDVAAPS 201
S +V K G+G VV V + D+A PS
Sbjct: 675 TLSWAVGDRVNHKKWGIGTVVSVKGGGDDQELDIAFPS 712
>gnl|CDD|192936 pfam12095, DUF3571, Protein of unknown function (DUF3571). This
family of proteins is functionally uncharacterized.
This protein is found in bacteria and eukaryotes.
Proteins in this family are typically between 85 to 97
amino acids in length.
Length = 83
Score = 32.2 bits (74), Expect = 0.044
Identities = 13/36 (36%), Positives = 24/36 (66%), Gaps = 4/36 (11%)
Query: 5 YLEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKT 40
+L+++L LDSLP +L + + LD++AQ ++ T
Sbjct: 32 WLKEWLTRLDSLPADLAKLPS----LDAQAQRLLDT 63
>gnl|CDD|238103 cd00176, SPEC, Spectrin repeats, found in several proteins involved
in cytoskeletal structure; family members include
spectrin, alpha-actinin and dystrophin; the spectrin
repeat forms a three helix bundle with the second helix
interrupted by proline in some sequences; the repeats
are independent folding units; tandem repeats are found
in differing numbers and arrange in an antiparallel
manner to form dimers; the repeats are defined by a
characteristic tryptophan (W) residue in helix A and a
leucine (L) at the carboxyl end of helix C and separated
by a linker of 5 residues; two copies of the repeat are
present here.
Length = 213
Score = 33.6 bits (77), Expect = 0.057
Identities = 15/70 (21%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 7 EQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAE 66
E L+S+ L+++ L EL++ + +K+++ +AE+ L+ + ++ +E L E
Sbjct: 132 EDLGKDLESVEELLKKHKELEEELEAH-EPRLKSLNELAEELLEEGHPDADEEIEEKLEE 190
Query: 67 IQKYFDKTKE 76
+ + +++ E
Sbjct: 191 LNERWEELLE 200
>gnl|CDD|164795 PHA00370, III, attachment protein.
Length = 297
Score = 33.4 bits (76), Expect = 0.092
Identities = 25/101 (24%), Positives = 37/101 (36%), Gaps = 27/101 (26%)
Query: 117 NTTGGAGGGGSGTGSGSGSAGGAASKSKRGRKKAK-----------------------DK 153
NT GG+GGG +G G GS GG + G+ K D
Sbjct: 104 NTGGGSGGGDTGGSGGGGSDGGGSEGGSTGKSLTKEGVGAGDFDYPKMANANKDALTEDN 163
Query: 154 AESATDAAGDDKSSNSKKKVAKKITG----VGGVVGVLNAI 190
++A D++ + V+ I+G VGG+V
Sbjct: 164 DQNALQKDADEQLDKASASVSDAISGFMRGVGGLVDNGGGE 204
Score = 28.0 bits (62), Expect = 5.8
Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 117 NTTGGAGGGGSGTG--SGSGSAGGAASKSKRG 146
GG G GGS TG +G G+ GG + G
Sbjct: 84 GDGGGTGEGGSDTGGDTGGGNTGGGSGGGDTG 115
Score = 27.6 bits (61), Expect = 7.7
Identities = 13/29 (44%), Positives = 15/29 (51%)
Query: 118 TTGGAGGGGSGTGSGSGSAGGAASKSKRG 146
T G GGG +G GSG G GG+ G
Sbjct: 96 TGGDTGGGNTGGGSGGGDTGGSGGGGSDG 124
>gnl|CDD|215565 PLN03083, PLN03083, E3 UFM1-protein ligase 1 homolog; Provisional.
Length = 803
Score = 33.3 bits (76), Expect = 0.13
Identities = 22/106 (20%), Positives = 44/106 (41%), Gaps = 13/106 (12%)
Query: 79 DDKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQEKALKNTTGGAGGGGSGTGSGSGSAGG 138
D K + ++ + + +I+ + + E+E+ +++ ++ G G S GS +
Sbjct: 356 DSKALILGESCVLSNGFIKGI---YDQIEKEMDAFSIQASSAG-LIGSSEKSLGSNESSP 411
Query: 139 AASKSKRGRKKAKDKAESATDAAGDD---------KSSNSKKKVAK 175
AAS S +G KK K K+ S + K +K +
Sbjct: 412 AASNSDKGSKKKKGKSTSTKGGTAESIPDDEEDAPKKGKKNQKKGR 457
Score = 29.0 bits (65), Expect = 2.6
Identities = 29/176 (16%), Positives = 53/176 (30%), Gaps = 35/176 (19%)
Query: 57 KDKKKETLAE--------IQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQ 108
KD K L E I+ +D+ ++ D +IQ +
Sbjct: 355 KDSKALILGESCVLSNGFIKGIYDQIEKEMDAF---SIQASSAGLIGSSEKSLG------ 405
Query: 109 EIQEKALKNTTGGAGGGGSGTGSGSGSAGGAAS-----------KSKRGRKKAKDKAESA 157
++ + G G + + GG A K K+ +KK +DK+
Sbjct: 406 --SNESSPAASNSDKGSKKKKGKSTSTKGGTAESIPDDEEDAPKKGKKNQKKGRDKSSKV 463
Query: 158 TDAAGDDKSSNSK--KKVAKKITGVGGVVGVLNAIVAADPDVAAPSHDVLDMPVDP 211
D K+ K K + + V+ I+ PD+ + +
Sbjct: 464 P---SDSKAGGKKESVKSQEDNNNIPPEEWVMKKILEWVPDLEEDGTEDPGSILKH 516
>gnl|CDD|220817 pfam10593, Z1, Z1 domain. This uncharacterized domain was
identified by Iyer and colleagues. It is found
associated with a helicase domain of superfamily type
II.
Length = 231
Score = 32.6 bits (75), Expect = 0.14
Identities = 18/70 (25%), Positives = 38/70 (54%), Gaps = 5/70 (7%)
Query: 32 SRAQDVMKTIDRVAEDYLDNMKHYSK--DKKKETLAEIQKYFDKTKEYGDDKVQLAIQTY 89
SR DV K + + E+YL++++ + D ET+AE+++ ++ E G D L ++
Sbjct: 34 SRFTDVHKQVADLIEEYLNSLRKAVENGDDLGETIAELKELYEDDFEPGTD---LDKPSW 90
Query: 90 EMVDKYIRKL 99
+ + + K+
Sbjct: 91 DEIQAALPKV 100
>gnl|CDD|217149 pfam02621, VitK2_biosynth, Menaquinone biosynthesis. This family
includes two enzymes which are involved in menaquinone
biosynthesis. One which catalyzes the conversion of
cyclic de-hypoxanthine futalosine to
1,4-dihydroxy-6-naphthoate, and one which may be
involved in the conversion of chorismate to futalosine.
These enzymes comprise two domains with alpha/beta
structures, a large domain and a small domain. A pocket
between the two domains may form the active site, a
conserved histidine located within this pocket could be
the catalytic base.
Length = 248
Score = 31.7 bits (73), Expect = 0.24
Identities = 16/71 (22%), Positives = 28/71 (39%), Gaps = 14/71 (19%)
Query: 55 YSKDKKKETLAEIQKYFDKTKEYGDDKVQLAIQTYEM---------VDKYIRKLDTDLAR 105
+D E E+++ K+KEY + + Y ++ Y+ +L DL
Sbjct: 175 VRRDLGLELAKELEEALRKSKEYALKHPEEIAE-YAAERAGLDEKFIELYVNELSYDLG- 232
Query: 106 FEQEIQEKALK 116
E KAL+
Sbjct: 233 ---EEGRKALR 240
>gnl|CDD|216689 pfam01765, RRF, Ribosome recycling factor. The ribosome recycling
factor (RRF / ribosome release factor) dissociates the
ribosome from the mRNA after termination of translation,
and is essential bacterial growth. Thus ribosomes are
"recycled" and ready for another round of protein
synthesis.
Length = 165
Score = 30.9 bits (71), Expect = 0.39
Identities = 20/76 (26%), Positives = 32/76 (42%), Gaps = 26/76 (34%)
Query: 35 QDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDK 94
+D + ++ +D K S+D+ K EIQK + DK
Sbjct: 115 RDANDKLKKLEKD-----KEISEDEVKRAEKEIQK---------------------LTDK 148
Query: 95 YIRKLDTDLARFEQEI 110
YI+K+D L + E+EI
Sbjct: 149 YIKKIDELLKKKEKEI 164
>gnl|CDD|216868 pfam02084, Bindin, Bindin.
Length = 239
Score = 31.4 bits (71), Expect = 0.41
Identities = 27/95 (28%), Positives = 39/95 (41%), Gaps = 10/95 (10%)
Query: 120 GGAGGGGSGTGSGSGSAGGAASKSKRGRKKAKDKAESATDAAGDDKSSNSKKKVAKKITG 179
GG GG G+G G+ G GG S G + A A DA + +S T
Sbjct: 41 GGGGGPGAGGGAPGGPVGGGGGGSG-GPPGGGEVAGEAEDAMSEFDDYSSSSIEEGDTTI 99
Query: 180 VGGVVGVLNAIVAADPDVAAPSHDVLDMPVDPNEP 214
V+ + A++ A +D+PVD N+P
Sbjct: 100 SADVMEKIKAVLGATK---------IDLPVDINDP 125
>gnl|CDD|218083 pfam04426, Bul1_C, Bul1 C terminus. This family contains the C
terminus of Saccharomyces cerevisiae Bul1. Bul1 binds
the ubiquitin ligase Rsp5, via an N terminal PPSY motif.
The complex containing Bul1 and Rsp5 is involved in
intracellular trafficking of the general amino acid
permease Gap1, degradation of Rog1 in cooperation with
Bul2 and GSK-3, and mitochondrial inheritance. Bul1 may
contain HEAT repeats.
Length = 226
Score = 30.4 bits (69), Expect = 0.63
Identities = 16/65 (24%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 12 SLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYF 71
S +S+PI+L LM + + +K I + +D+L +K Y K K E ++ + +
Sbjct: 58 SDNSIPIKLNSEL-LMNK------EKLKNIKKTFKDFLKKIKEY-KKKFNENKEKLNELY 109
Query: 72 DKTKE 76
+ +
Sbjct: 110 NLNRT 114
>gnl|CDD|221517 pfam12300, DUF3628, Protein of unknown function (DUF3628). This
domain family is found in bacteria, and is typically
between 153 and 183 amino acids in length. The family is
found in association with pfam00270, pfam00271.
Length = 180
Score = 30.4 bits (68), Expect = 0.64
Identities = 19/68 (27%), Positives = 25/68 (36%), Gaps = 5/68 (7%)
Query: 123 GGGGSGTGSGSGSAGGAASKSKRG-----RKKAKDKAESATDAAGDDKSSNSKKKVAKKI 177
GGG SG G SG G + G R K + E D+A D + A +
Sbjct: 57 GGGRSGPGERSGRPVGKGPRDGDGGGGRRRGPRKPRLEGERDSAADGAVTPVFGASAPRP 116
Query: 178 TGVGGVVG 185
G+ G
Sbjct: 117 PGIVAAPG 124
Score = 27.7 bits (61), Expect = 4.9
Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 1/59 (1%)
Query: 104 ARFEQEIQEKALKNTTGGAGGGGSGTGSGSGSAGGAASKSKRGRKKAKDKAESATDAAG 162
R QE + ++ G G G G G GG + R + + + + +SA D A
Sbjct: 48 VRAAQEWRRGGGRSGPGERSGRPVGKGPRDGDGGGGRRRGPR-KPRLEGERDSAADGAV 105
>gnl|CDD|223311 COG0233, Frr, Ribosome recycling factor [Translation, ribosomal
structure and biogenesis].
Length = 187
Score = 30.2 bits (69), Expect = 0.66
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 10/81 (12%)
Query: 33 RAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDD---KVQLAIQTY 89
R ++++K + AE+ +++ +D + K +K KE +D K + IQ
Sbjct: 111 RRKELVKVAKKYAEEAKVAVRNIRRDANDKI-----KKLEKDKEISEDEVKKAEEEIQK- 164
Query: 90 EMVDKYIRKLDTDLARFEQEI 110
+ D+YI+K+D L E+EI
Sbjct: 165 -LTDEYIKKIDELLKDKEKEI 184
>gnl|CDD|239131 cd02666, Peptidase_C19J, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 343
Score = 30.5 bits (69), Expect = 0.71
Identities = 21/86 (24%), Positives = 34/86 (39%), Gaps = 13/86 (15%)
Query: 6 LEQY--LDSLDSLPIELQ-----RNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSK- 57
L++Y DSL LP Q + ++ +ID + E + ++ S
Sbjct: 195 LDRYFDYDSLTKLPQRSQVQAQLAQPLQRELISMDRYELPSSIDDIDELIREAIQSESSL 254
Query: 58 -----DKKKETLAEIQKYFDKTKEYG 78
++ E EI+K FD K YG
Sbjct: 255 VRQAQNELAELKHEIEKQFDDLKSYG 280
>gnl|CDD|213033 cd11725, ADDz_Dnmt3, ADDz domain of DNA (cytosine-5)
methyltransferases (C5-MTases) 3 (Dnmt3). Dnmt3 is a de
novo DNA methyltransferase family that includes two
active enzymes Dnmt3a and -3b and one regulatory factor
Dnmt3l. The ADDz domain of Dnmt3 is located in the
C-terminal region of Dnmt3, which is an active catalytic
domain in Dnmt3a and -b, but lacks some residues for
enzymatic activity in Dnmt3l. DNA methylation is an
important epigenetic mechanism involved in diverse
biological processes such as embryonic development, gene
expression, and genomic imprinting. The ADDz_Dnmt3
domain is a PHD-like zinc finger motif that contains two
parts, a C2-C2 and a PHD-like zinc finger. PHD zinc
finger domains have been identified in more than 40
proteins that are mainly involved in chromatin mediated
transcriptional control; the classical PHD zinc finger
has a C4-H-C3 motif that spans about 50-80 amino acids.
In ADDz, the conserved histidine residue of the PHD
finger is replaced by a cysteine, and an additional zinc
finger C2-C2 like motif is located about twenty residues
upstream of the C4-C-C3 motif.
Length = 126
Score = 29.5 bits (67), Expect = 0.81
Identities = 14/51 (27%), Positives = 19/51 (37%), Gaps = 12/51 (23%)
Query: 216 YC-VCQQVSYGEMIGCDNPDCPIEWFHFACV--------SLTTKPKGKWYC 257
YC +C GE+I CDN C + AC+ + W C
Sbjct: 49 YCTIC--CGGGEVILCDNESCC-RVYCTACLDILVGPGTYDKVLLEDPWSC 96
>gnl|CDD|173502 PTZ00266, PTZ00266, NIMA-related protein kinase; Provisional.
Length = 1021
Score = 30.5 bits (68), Expect = 0.94
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 7/50 (14%)
Query: 105 RFEQEIQEKALKNT-------TGGAGGGGSGTGSGSGSAGGAASKSKRGR 147
R E++ EKA +N+ G + GGG G G G G+ GA + GR
Sbjct: 514 RLERDRLEKARRNSYFLKGMENGLSAGGGPGDGPGVGAGVGAGVGTSDGR 563
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 30.2 bits (68), Expect = 1.1
Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 1/59 (1%)
Query: 110 IQEKALKNTTGGAGGGGSGTGSGSGSAGGAASKSK-RGRKKAKDKAESATDAAGDDKSS 167
I+ + ++N GGGG G G G G G + + + + AE + GD K +
Sbjct: 382 IKAEPIQNGRQQRGGGGRGQGGGRGQQQGQPRRGEGGAKSASAKPAEKPSRRLGDAKPA 440
Score = 29.0 bits (65), Expect = 3.0
Identities = 10/55 (18%), Positives = 16/55 (29%)
Query: 120 GGAGGGGSGTGSGSGSAGGAASKSKRGRKKAKDKAESATDAAGDDKSSNSKKKVA 174
G GGG G A + + + AG+ + +K A
Sbjct: 399 RGQGGGRGQQQGQPRRGEGGAKSASAKPAEKPSRRLGDAKPAGEQQRRRRPRKPA 453
>gnl|CDD|128778 smart00502, BBC, B-Box C-terminal domain. Coiled coil region
C-terminal to (some) B-Box domains.
Length = 127
Score = 29.2 bits (66), Expect = 1.1
Identities = 11/57 (19%), Positives = 23/57 (40%), Gaps = 12/57 (21%)
Query: 3 TSYLEQYLDSLDSLPIELQRN------------FTLMRELDSRAQDVMKTIDRVAED 47
+ LE L L S+ E++ N L L+ R + +++ ++ E+
Sbjct: 16 AAELEDALKQLISIIQEVEENAADVEAQIKAAFDELRNALNKRKKQLLEDLEEQKEN 72
>gnl|CDD|218169 pfam04604, L_biotic_typeA, Type-A lantibiotic. Lantibiotics are
antibiotic peptides distinguished by the presence of the
rare thioether amino acids lanthionine and/or
methyl-lanthionine. They are produced by Gram-positive
bacteria as gene-encoded precursor peptides and undergo
post-translational modification to generate the mature
peptide. Based on their structural and functional
features lantibiotics are currently divided into two
major groups: the flexible amphiphilic type-A and the
rather rigid and globular type-B. Type-A lantibiotics
act primarily by pore formation in the bacterial
membrane by a mechanism involving the interaction with
specific docking molecules such as the membrane
precursor lipid II.
Length = 50
Score = 27.4 bits (61), Expect = 1.3
Identities = 10/29 (34%), Positives = 13/29 (44%)
Query: 101 TDLARFEQEIQEKALKNTTGGAGGGGSGT 129
T+ QE+ E+ L GG G G T
Sbjct: 5 TEALNSLQEVSEEELDQILGGKGSGVIKT 33
>gnl|CDD|237034 PRK12278, PRK12278, 50S ribosomal protein L21/unknown domain fusion
protein; Provisional.
Length = 221
Score = 29.4 bits (66), Expect = 1.4
Identities = 19/78 (24%), Positives = 31/78 (39%), Gaps = 4/78 (5%)
Query: 128 GTGSGSGSAGGAASKSKRGRKKAKDKAESATDAAGDDKSSNSKKKVAKKITGVGGVVG-- 185
G G +A A +K+K+ A +A A ++ + KITGVG +
Sbjct: 116 GAGKVEVAAEAAPAKAKKEAAPKAAPAPAAAAAP--PAAAAAGADDLTKITGVGPALAKK 173
Query: 186 VLNAIVAADPDVAAPSHD 203
+ A V +AA +
Sbjct: 174 LNEAGVTTFAQIAALTDA 191
>gnl|CDD|213032 cd11672, ADDz, ADDz for ATRX, Dnmt3 and Dnmt3l PHD-like zinc finger
domain. The ADDz zinc finger domain is present in the
chromatin-associated proteins
cytosine-5-methyltransferase 3 (Dnmt3) and ATRX, a SNF2
type transcription factor protein. The Dnmt3 family
includes two active DNA methyltransferases, Dnmt3a and
-3b, and one regulatory factor Dnmt3l. DNA methylation
is an important epigenetic mechanism involved in diverse
biological processes such as embryonic development, gene
expression, and genomic imprinting. The ADDz domain is a
PHD-like zinc finger motif that contains two parts, a
C2-C2 and a PHD-like zinc finger. PHD zinc finger
domains have been identified in more than 40 proteins
that are mainly involved in chromatin mediated
transcriptional control; the classical PHD zinc finger
has a C4-H-C3 motif that spans about 50-80 amino acids.
In ADDz, the conserved histidine residue of the PHD
finger is replaced by a cysteine, and an additional zinc
finger C2-C2 like motif is located about twenty residues
upstream of the C4-C-C3 motif.
Length = 120
Score = 28.8 bits (65), Expect = 1.4
Identities = 14/51 (27%), Positives = 19/51 (37%), Gaps = 12/51 (23%)
Query: 216 YC-VCQQVSYGEMIGCDNPDCPIEWFHFACV--------SLTTKPKGKWYC 257
YC +C GE+I CDN C + AC+ + W C
Sbjct: 49 YCTIC--CGGGEVILCDNESCC-RVYCTACLDFLVGPGTYDKVLDEDPWSC 96
>gnl|CDD|221581 pfam12446, DUF3682, Protein of unknown function (DUF3682). This
domain family is found in eukaryotes, and is typically
between 125 and 136 amino acids in length.
Length = 133
Score = 28.6 bits (64), Expect = 1.5
Identities = 14/49 (28%), Positives = 20/49 (40%)
Query: 121 GAGGGGSGTGSGSGSAGGAASKSKRGRKKAKDKAESATDAAGDDKSSNS 169
G GG SG+ + + AG + A SA + G+ SS S
Sbjct: 6 GTGGVSSGSSAPAPPAGPGPGPNAPPAPAAPGVDSSAGSSGGEAGSSGS 54
>gnl|CDD|107029 PHA01351, PHA01351, putative minor structural protein.
Length = 1070
Score = 29.9 bits (67), Expect = 1.5
Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 17/85 (20%)
Query: 16 LPIELQR---NFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFD 72
+P ELQ + R + +++ TI+ + E K K L Q Y
Sbjct: 998 IPQELQNTYFEYARNRRVSRYVNEIITTINLLFE------------KHKIDLDTAQSYLQ 1045
Query: 73 KTKEYG--DDKVQLAIQTYEMVDKY 95
+ K+YG D+++QL +++ Y
Sbjct: 1046 QLKKYGLTDEEIQLIKLNWQLRSAY 1070
>gnl|CDD|226642 COG4174, COG4174, ABC-type uncharacterized transport system,
permease component [General function prediction only].
Length = 364
Score = 29.7 bits (67), Expect = 1.6
Identities = 13/45 (28%), Positives = 17/45 (37%), Gaps = 5/45 (11%)
Query: 107 EQEIQEKALKNTTGGA---GGGGSGTGSGSGSAGGAASKSKRGRK 148
EQ I + L+ G GGGG G G + RG +
Sbjct: 36 EQAIAK--LEGGQSGLDRLGGGGVDASGAGGGVGNISDSQYRGAQ 78
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 30.1 bits (68), Expect = 1.6
Identities = 22/116 (18%), Positives = 58/116 (50%), Gaps = 3/116 (2%)
Query: 6 LEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYS--KDKKKET 63
LE+ LD+L EL+ L+ +++ + I+ + E + + + + +E
Sbjct: 802 LEEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEEL 861
Query: 64 LAEIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQEKALKNTT 119
E+++ + +E D+ +L + E +++ +R+L+++LA ++EI++ +
Sbjct: 862 KEELEELEAEKEELEDELKELE-EEKEELEEELRELESELAELKEEIEKLRERLEE 916
>gnl|CDD|233237 TIGR01026, fliI_yscN, ATPase FliI/YscN family. This family of
ATPases demonstrates extensive homology with ATP
synthase F1, beta subunit. It is a mixture of members
with two different protein functions. The first group is
exemplified by Salmonella typhimurium FliI protein. It
is needed for flagellar assembly, its ATPase activity is
required for flagellation, and it may be involved in a
specialized protein export pathway that proceeds without
signal peptide cleavage. The second group of proteins
function in the export of virulence proteins;
exemplified by Yersinia sp. YscN protein an ATPase
involved in the type III secretory pathway for the
antihost Yops proteins [Energy metabolism, ATP-proton
motive force interconversion].
Length = 440
Score = 29.6 bits (67), Expect = 1.6
Identities = 22/96 (22%), Positives = 45/96 (46%), Gaps = 9/96 (9%)
Query: 26 LMRELDSR----AQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFD--KTKEY-- 77
L R L R A DV+ +I R+ + + K +E L++ + D + Y
Sbjct: 339 LSRALAQRGHYPAIDVLASISRLMTAIVSEEHRRAARKFRELLSKYKDNEDLIRIGAYQR 398
Query: 78 GDDK-VQLAIQTYEMVDKYIRKLDTDLARFEQEIQE 112
G D+ + AI Y +++++++ + FE+ +Q+
Sbjct: 399 GSDRELDFAIAKYPKLERFLKQGINEKVNFEESLQQ 434
>gnl|CDD|131611 TIGR02560, HrpB4, type III secretion protein HrpB4. This family of
genes are always found in type III secretion operons in
a limited number of species including Burkholderia,
Xanthomonas and Ralstonia.
Length = 210
Score = 29.1 bits (65), Expect = 1.6
Identities = 17/48 (35%), Positives = 20/48 (41%)
Query: 2 STSYLEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYL 49
S S L + + L LP L MR L SR V + IDR L
Sbjct: 65 SLSALLERANRLAVLPPALLLRVLRMRALFSRRTAVRRCIDRARLSRL 112
>gnl|CDD|227594 COG5269, ZUO1, Ribosome-associated chaperone zuotin [Translation,
ribosomal structure and biogenesis / Posttranslational
modification, protein turnover, chaperones].
Length = 379
Score = 29.6 bits (66), Expect = 1.9
Identities = 41/175 (23%), Positives = 73/175 (41%), Gaps = 20/175 (11%)
Query: 36 DVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDKY 95
D +T + + EDY D+M+ +D+K+ + A+ ++ K K + +++ +Q + D
Sbjct: 174 DSWRTFEPLDEDYPDDME--ERDRKRYSEAKNREKRAKLKNQDNARLKRLVQIAKKRDPR 231
Query: 96 IRKLDTDLARFEQEIQEKALKNTTGGAGGGGSGTGSGSGSAGGAASKSKRGRKKAKDKAE 155
I+ EQE + K ++ AG A A + +G+ +AK+KAE
Sbjct: 232 IKSFK------EQEKEMKKIRKWEREAG------------ARLKALAALKGKAEAKNKAE 273
Query: 156 SATDAAGDDKSSNSKKKVAKKITGVGGVVGVLNAIVAADPDVAAPSHDVLDMPVD 210
+A + K K K + NA AD A + +D VD
Sbjct: 274 IEAEALASATAVKKKAKEVMKKALKMEKKAIKNAAKDADYFGDADKAEHIDEDVD 328
>gnl|CDD|221084 pfam11336, DUF3138, Protein of unknown function (DUF3138). This
family of proteins with unknown function appear to be
restricted to Proteobacteria.
Length = 514
Score = 29.5 bits (66), Expect = 2.0
Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 2/50 (4%)
Query: 96 IRKLDTDLARFEQEIQE--KALKNTTGGAGGGGSGTGSGSGSAGGAASKS 143
I+ L L +Q++ E AL AGGG + + +A +S +
Sbjct: 27 IKALQAQLTALQQQVNELRAALAAKPAAAGGGAKIQSAAAAAAAAPSSDA 76
>gnl|CDD|236092 PRK07772, PRK07772, single-stranded DNA-binding protein;
Provisional.
Length = 186
Score = 28.8 bits (65), Expect = 2.1
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 117 NTTGGAGGGGSGTGSGSGSAGGAAS 141
GG GGGG G+G G G GG +
Sbjct: 128 GGGGGFGGGGGGSGGGGGGGGGGGA 152
Score = 28.5 bits (64), Expect = 2.6
Identities = 15/48 (31%), Positives = 17/48 (35%)
Query: 120 GGAGGGGSGTGSGSGSAGGAASKSKRGRKKAKDKAESATDAAGDDKSS 167
GG GGG G G G G G + A D SA + G
Sbjct: 134 GGGGGGSGGGGGGGGGGGAPGGGGAQASAPADDPWSSAPASGGFGGGD 181
Score = 28.5 bits (64), Expect = 2.9
Identities = 17/45 (37%), Positives = 21/45 (46%), Gaps = 2/45 (4%)
Query: 120 GGAGGGGSGTGSGSGSAGGAASKSKRGRKKAKDKAESATDAAGDD 164
GG GGGG G G G G +GG G A+++ A DD
Sbjct: 124 GGGGGGGGGFGGGGGGSGGGGGGGGGGGAPGGGGAQAS--APADD 166
>gnl|CDD|211826 TIGR03497, FliI_clade2, flagellar protein export ATPase FliI.
Members of this protein family are the FliI protein of
bacterial flagellum systems. This protein acts to drive
protein export for flagellar biosynthesis. The most
closely related family is the YscN family of bacterial
type III secretion systems. This model represents one
(of three) segment of the FliI family tree. These have
been modeled separately in order to exclude the type III
secretion ATPases more effectively [Cellular processes,
Chemotaxis and motility].
Length = 413
Score = 29.2 bits (66), Expect = 2.1
Identities = 21/101 (20%), Positives = 43/101 (42%), Gaps = 17/101 (16%)
Query: 24 FTLMRELDSRAQ----DVMKTIDRVAEDYLDN---------MKHYSKDKKKETLAEIQKY 70
L REL ++ DV+ ++ RV + + + + K+ E L I Y
Sbjct: 311 IVLSRELAAKNHYPAIDVLASVSRVMNEIVSEEHKELAGKLRELLAVYKEAEDLINIGAY 370
Query: 71 FDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQ 111
K + K+ AI+ E ++ ++++ + FE+ +Q
Sbjct: 371 ----KRGSNPKIDEAIRYIEKINSFLKQGIDEKFTFEETVQ 407
>gnl|CDD|237537 PRK13875, PRK13875, conjugal transfer protein TrbL; Provisional.
Length = 440
Score = 29.1 bits (66), Expect = 2.2
Identities = 8/43 (18%), Positives = 11/43 (25%)
Query: 120 GGAGGGGSGTGSGSGSAGGAASKSKRGRKKAKDKAESATDAAG 162
G G G SA + + R K+ A
Sbjct: 335 AGVAAGLGGVARAGASAAASPLRRAASRAAESMKSSFRAGARS 377
Score = 29.1 bits (66), Expect = 2.6
Identities = 13/44 (29%), Positives = 19/44 (43%), Gaps = 1/44 (2%)
Query: 120 GGAGGGGSGTGS-GSGSAGGAASKSKRGRKKAKDKAESATDAAG 162
GA G +G G A AAS +R +A + +S+ A
Sbjct: 332 SGAAGVAAGLGGVARAGASAAASPLRRAASRAAESMKSSFRAGA 375
Score = 27.6 bits (62), Expect = 7.4
Identities = 23/83 (27%), Positives = 30/83 (36%), Gaps = 5/83 (6%)
Query: 118 TTGGAGGGGSGTGSGSGSAGGAASKSKRGRKKAKDKAESATDAAGDDKSSNSKKKVAKKI 177
T AGG +G+G A G + + G A A AAG S+ S
Sbjct: 277 TGLAAGGAAVAAAAGAGLAAGGGAAAAGGAAAA---ARGGAAAAGGASSAYSAGAAGG-- 331
Query: 178 TGVGGVVGVLNAIVAADPDVAAP 200
+G GV L + A AA
Sbjct: 332 SGAAGVAAGLGGVARAGASAAAS 354
>gnl|CDD|178850 PRK00083, frr, ribosome recycling factor; Reviewed.
Length = 185
Score = 28.5 bits (65), Expect = 2.3
Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 26/76 (34%)
Query: 35 QDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDK 94
+D + ++ +D K S+D+ K EIQK + DK
Sbjct: 133 RDANDKLKKLEKD-----KEISEDELKRAEDEIQK---------------------LTDK 166
Query: 95 YIRKLDTDLARFEQEI 110
YI+K+D LA E+EI
Sbjct: 167 YIKKIDELLAAKEKEI 182
>gnl|CDD|182507 PRK10510, PRK10510, putative outer membrane lipoprotein;
Provisional.
Length = 219
Score = 28.7 bits (64), Expect = 2.3
Identities = 14/29 (48%), Positives = 17/29 (58%)
Query: 121 GAGGGGSGTGSGSGSAGGAASKSKRGRKK 149
G G G+G GS G+ GA S SK+ R K
Sbjct: 33 GKSGIGAGIGSLVGAGIGALSSSKKDRGK 61
>gnl|CDD|100109 cd05831, Ribosomal_P1, Ribosomal protein P1. This subfamily
represents the eukaryotic large ribosomal protein P1.
Eukaryotic P1 and P2 are functionally equivalent to the
bacterial protein L7/L12, but are not homologous to
L7/L12. P1 is located in the L12 stalk, with proteins
P2, P0, L11, and 28S rRNA. P1 and P2 are the only
proteins in the ribosome to occur as multimers, always
appearing as sets of heterodimers. Recent data indicate
that eukaryotes have four copies (two heterodimers),
while most archaeal species contain six copies of L12p
(three homodimers) and bacteria may have four or six
copies (two or three homodimers), depending on the
species. Experiments using S. cerevisiae P1 and P2
indicate that P1 proteins are positioned more internally
with limited reactivity in the C-terminal domains, while
P2 proteins seem to be more externally located and are
more likely to interact with other cellular components.
In lower eukaryotes, P1 and P2 are further subdivided
into P1A, P1B, P2A, and P2B, which form P1A/P2B and
P1B/P2A heterodimers. Some plant species have a third
P-protein, called P3, which is not homologous to P1 and
P2. In humans, P1 and P2 are strongly autoimmunogenic.
They play a significant role in the etiology and
pathogenesis of systemic lupus erythema (SLE). In
addition, the ribosome-inactivating protein
trichosanthin (TCS) interacts with human P0, P1, and P2,
with its primary binding site located in the C-terminal
region of P2. TCS inactivates the ribosome by
depurinating a specific adenine in the sarcin-ricin loop
of 28S rRNA.
Length = 103
Score = 27.7 bits (62), Expect = 2.4
Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 7/55 (12%)
Query: 112 EKALKN-------TTGGAGGGGSGTGSGSGSAGGAASKSKRGRKKAKDKAESATD 159
KAL+ + G GGGG+ + + +A AA+++K+ KK +++ ES D
Sbjct: 43 AKALEGKDIKDLLSNVGGGGGGAAPAAAAAAAAAAAAEAKKEEKKEEEEEESDDD 97
Score = 26.5 bits (59), Expect = 5.9
Identities = 14/54 (25%), Positives = 30/54 (55%)
Query: 106 FEQEIQEKALKNTTGGAGGGGSGTGSGSGSAGGAASKSKRGRKKAKDKAESATD 159
F + ++ K +K+ GGGG G + +A AA+ ++ +++ K++ E +D
Sbjct: 42 FAKALEGKDIKDLLSNVGGGGGGAAPAAAAAAAAAAAAEAKKEEKKEEEEEESD 95
>gnl|CDD|218967 pfam06273, eIF-4B, Plant specific eukaryotic initiation factor 4B.
This family consists of several plant specific
eukaryotic initiation factor 4B proteins.
Length = 496
Score = 28.9 bits (64), Expect = 2.6
Identities = 15/46 (32%), Positives = 19/46 (41%), Gaps = 1/46 (2%)
Query: 119 TGGAGGGGSGTGSGSGSAGGAASKSKR-GRKKAKDKAESATDAAGD 163
GG GGGG SG A S R GRKK + + + +
Sbjct: 189 GGGGGGGGGERRSGGFRDSPGADDSDRWGRKKVETFGSAFGENGEE 234
>gnl|CDD|180777 PRK06958, PRK06958, single-stranded DNA-binding protein;
Provisional.
Length = 182
Score = 28.6 bits (64), Expect = 2.6
Identities = 11/29 (37%), Positives = 13/29 (44%)
Query: 120 GGAGGGGSGTGSGSGSAGGAASKSKRGRK 148
GG+GGGG G G GG G +
Sbjct: 112 GGSGGGGGGGDEGGYGGGGGGGGGGYGGE 140
Score = 27.8 bits (62), Expect = 4.8
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 119 TGGAGGGGSGTGSGSGSAGGAASKS 143
G GGG + G G G+ GGA+ S
Sbjct: 142 RSGGGGGRASGGGGGGAGGGASRPS 166
Score = 27.5 bits (61), Expect = 6.3
Identities = 11/28 (39%), Positives = 11/28 (39%)
Query: 120 GGAGGGGSGTGSGSGSAGGAASKSKRGR 147
GG GG G G G G GG R
Sbjct: 117 GGGGGDEGGYGGGGGGGGGGYGGESRSG 144
Score = 27.1 bits (60), Expect = 8.3
Identities = 18/44 (40%), Positives = 19/44 (43%)
Query: 120 GGAGGGGSGTGSGSGSAGGAASKSKRGRKKAKDKAESATDAAGD 163
GG GGGG G G S S GG S G A A + AG
Sbjct: 128 GGGGGGGGGYGGESRSGGGGGRASGGGGGGAGGGASRPSAPAGG 171
>gnl|CDD|117316 pfam08746, zf-RING-like, RING-like domain. This is a zinc finger
domain that is related to the C3HC4 RING finger domain
(pfam00097).
Length = 43
Score = 26.2 bits (58), Expect = 2.7
Identities = 8/18 (44%), Positives = 9/18 (50%), Gaps = 1/18 (5%)
Query: 228 IGCDNPDCPIEWFHFACV 245
C N DC I W H C+
Sbjct: 12 QRCGNRDCNIRW-HVDCL 28
>gnl|CDD|149112 pfam07863, CtnDOT_TraJ, Homologues of TraJ from Bacteroides
conjugative transposon. Members of this family have
been implicated in as being involved in an unusual form
of DNA transfer (conjugation) in Bacteroides. The family
has been named CtnDOT_TraJ to avoid confusion with other
conjugative transfer systems.
Length = 61
Score = 26.5 bits (59), Expect = 3.0
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 116 KNTTGGAGGGGSGTGSGSGSAGGAASKSKRGR 147
+N AG GGS +G+G+A G A+ RG+
Sbjct: 30 RNVNSTAGRGGSSAAAGAGAAMGNAAGRLRGK 61
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional.
Length = 293
Score = 28.5 bits (64), Expect = 3.0
Identities = 10/23 (43%), Positives = 10/23 (43%)
Query: 120 GGAGGGGSGTGSGSGSAGGAASK 142
GG G G G G G G GG
Sbjct: 33 GGRGRGRGGGGGGRGGGGGGGPG 55
Score = 28.2 bits (63), Expect = 4.5
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 120 GGAGGGGSGTGSGSGSAGGAASKSKRGRK 148
GG GGGG G G G GG + + G
Sbjct: 15 GGGGGGGRGGGGRGGGRGGGRGRGRGGGG 43
Score = 28.2 bits (63), Expect = 4.6
Identities = 12/32 (37%), Positives = 14/32 (43%)
Query: 120 GGAGGGGSGTGSGSGSAGGAASKSKRGRKKAK 151
GG GGG G G G GG GR + +
Sbjct: 8 GGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGR 39
Score = 28.2 bits (63), Expect = 4.8
Identities = 12/31 (38%), Positives = 14/31 (45%)
Query: 120 GGAGGGGSGTGSGSGSAGGAASKSKRGRKKA 150
GG GGG G G G G GG + G +
Sbjct: 3 GGGFGGGRGGGRGGGGGGGRGGGGRGGGRGG 33
Score = 27.8 bits (62), Expect = 6.5
Identities = 10/32 (31%), Positives = 10/32 (31%)
Query: 120 GGAGGGGSGTGSGSGSAGGAASKSKRGRKKAK 151
GG GGG G GG G K
Sbjct: 25 GGRGGGRGGGRGRGRGGGGGGRGGGGGGGPGK 56
Score = 27.4 bits (61), Expect = 7.2
Identities = 11/32 (34%), Positives = 13/32 (40%)
Query: 120 GGAGGGGSGTGSGSGSAGGAASKSKRGRKKAK 151
G G GG G G G GG RG + +
Sbjct: 6 FGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGR 37
>gnl|CDD|218573 pfam05387, Chorion_3, Chorion family 3. This family consists of
several Drosophila chorion proteins S36 and S38. The
chorion genes of Drosophila are amplified in response to
developmental signals in the follicle cells of the
ovary.
Length = 277
Score = 28.5 bits (63), Expect = 3.1
Identities = 21/70 (30%), Positives = 28/70 (40%), Gaps = 1/70 (1%)
Query: 120 GGAGGGGSGTGSGSGSAGGAASKSKRGRKKAKDKAESATDAAGDDKSSNSKKKVAKKITG 179
G AGGGG G GSG AG +A + A S + G + A ++
Sbjct: 21 GSAGGGG-GHGSGQYGAGASAGLEEYVNAAAGGAQPSGGNIIGAQAEIQPTPEEAGRLGR 79
Query: 180 VGGVVGVLNA 189
V + LNA
Sbjct: 80 VQAQLQALNA 89
>gnl|CDD|224429 COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase
type [General function prediction only].
Length = 271
Score = 28.5 bits (64), Expect = 3.2
Identities = 11/33 (33%), Positives = 15/33 (45%)
Query: 116 KNTTGGAGGGGSGTGSGSGSAGGAASKSKRGRK 148
+++ G GG G SG G +GG S G
Sbjct: 236 RSSGSGGSGGSGGGSSGGGFSGGGGSSGGGGAS 268
Score = 28.1 bits (63), Expect = 4.0
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 119 TGGAGGGGSGTGSGSGSAGGAASKS 143
+GG GG +G G S GG AS S
Sbjct: 246 SGGGSSGGGFSGGGGSSGGGGASGS 270
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 28.9 bits (65), Expect = 3.2
Identities = 23/113 (20%), Positives = 55/113 (48%), Gaps = 11/113 (9%)
Query: 6 LEQYLDSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLA 65
LE+Y L + EL+ R+L +++ K + + +E K KE
Sbjct: 454 LEEYTAELKRIEKELKEIEEKERKLRKELRELEKVLKKESELI----------KLKELAE 503
Query: 66 EIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQE-KALKN 117
++++ +K K+Y ++++ + YE + + + KL ++ ++E+++ + LK
Sbjct: 504 QLKELEEKLKKYNLEELEKKAEEYEKLKEKLIKLKGEIKSLKKELEKLEELKK 556
>gnl|CDD|227244 COG4907, COG4907, Predicted membrane protein [Function unknown].
Length = 595
Score = 28.7 bits (64), Expect = 3.3
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 116 KNTTGGAGGGGSGTGSGSGSAGG 138
++++ G GGG SG GSG G G
Sbjct: 572 RSSSSGGGGGFSGGGSGGGGGGA 594
Score = 28.0 bits (62), Expect = 6.6
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 120 GGAGGGGSGTGSGSGSAGGAA 140
+GGGG +G GSG GG A
Sbjct: 574 SSSGGGGGFSGGGSGGGGGGA 594
>gnl|CDD|221784 pfam12810, Gly_rich, Glycine rich protein. This family of proteins
is greatly expanded in Trichomonas vaginalis. The
proteins are composed of several glycine rich motifs
interspersed through the sequence. Although many
proteins have been annotated by similarity in the family
these annotations given the biased composition of the
sequences these are unlikely to be functionally
relevant.
Length = 248
Score = 28.3 bits (64), Expect = 3.4
Identities = 9/19 (47%), Positives = 10/19 (52%)
Query: 120 GGAGGGGSGTGSGSGSAGG 138
GG GG G+ G G GG
Sbjct: 112 GGGGGSGNYNGGSGGFGGG 130
>gnl|CDD|222632 pfam14260, zf-C4pol, C4-type zinc-finger of DNA polymerase delta.
In fission yeast this zinc-finger domain appears is the
region of Pol3 that binds directly to the B-subunit,
Cdc1. Pol delta is a hetero-tetrameric enzyme comprising
four evolutionarily well-conserved proteins: the
catalytic subunit Pol3 and three smaller subunits Cdc1,
Cdc27 and Cdm1.
Length = 73
Score = 26.6 bits (59), Expect = 3.5
Identities = 10/22 (45%), Positives = 14/22 (63%), Gaps = 2/22 (9%)
Query: 218 VCQ--QVSYGEMIGCDNPDCPI 237
+CQ Q S E + CD+ DCP+
Sbjct: 47 ICQRCQGSLHEEVLCDSRDCPV 68
>gnl|CDD|184923 PRK14959, PRK14959, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 624
Score = 28.9 bits (64), Expect = 3.5
Identities = 13/45 (28%), Positives = 18/45 (40%)
Query: 123 GGGGSGTGSGSGSAGGAASKSKRGRKKAKDKAESATDAAGDDKSS 167
GGG+ SGS + G A+ + + AAG SS
Sbjct: 374 SGGGASAPSGSAAEGPASGGAATIPTPGTQGPQGTAPAAGMTPSS 418
Score = 28.5 bits (63), Expect = 4.1
Identities = 11/46 (23%), Positives = 20/46 (43%), Gaps = 2/46 (4%)
Query: 119 TGGAGGGGSGTGSGSGSAGGAASKSKRG--RKKAKDKAESATDAAG 162
+GG SG+ + ++GGAA+ G + A T ++
Sbjct: 374 SGGGASAPSGSAAEGPASGGAATIPTPGTQGPQGTAPAAGMTPSSA 419
>gnl|CDD|203394 pfam06133, DUF964, Protein of unknown function (DUF964). This
family consists of several relatively short bacterial
and archaeal hypothetical sequences. The function of
this family is unknown.
Length = 108
Score = 27.5 bits (62), Expect = 3.6
Identities = 9/43 (20%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 31 DSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDK 73
D AQ ++ ++ E+ + + K+ KE +IQ+ +
Sbjct: 32 DEEAQKLIDEFQKLQEEI-QEKQMFGKEIPKEVQQKIQELKRE 73
>gnl|CDD|224212 COG1293, COG1293, Predicted RNA-binding protein homologous to
eukaryotic snRNP [Transcription].
Length = 564
Score = 28.5 bits (64), Expect = 3.8
Identities = 30/125 (24%), Positives = 48/125 (38%), Gaps = 14/125 (11%)
Query: 5 YLEQYLDSLDSLPIELQRNFTLMRELDSRAQ---DVMKTIDRVAEDYLDNMKHYSKDKKK 61
LE+ D L+ L + L + Q + +K++ R+A+ Y + DK K
Sbjct: 301 KLEKQEDELEELEKAAEELRQKGELLYANLQLIEEGLKSV-RLADFYGNEEIKIELDKSK 359
Query: 62 ETLAEIQKYFDKTKEYGDDKVQL---------AIQTYEMVDKYIRKLDTDLARFEQEIQE 112
Q+YF K K+ KV L AI YE + K + A E+ +E
Sbjct: 360 TPSENAQRYFKKYKKLKGAKVNLDRQLSELKEAIAYYESAKTALEKAEGKKA-IEEIREE 418
Query: 113 KALKN 117
+
Sbjct: 419 LIEEG 423
>gnl|CDD|234336 TIGR03734, PRTRC_parB, PRTRC system ParB family protein. A novel
genetic system characterized by six major proteins,
included a ParB homolog and a ThiF homolog, is
designated PRTRC, or ParB-Related,ThiF-Related Cassette.
It is often found on plasmids. This protein family the
member related to ParB, and is designated PRTRC system
ParB family protein.
Length = 554
Score = 28.5 bits (64), Expect = 3.9
Identities = 9/48 (18%), Positives = 17/48 (35%)
Query: 108 QEIQEKALKNTTGGAGGGGSGTGSGSGSAGGAASKSKRGRKKAKDKAE 155
+ A + A G G+ S + + +K KKA ++
Sbjct: 325 ERAAAAAAQKPAAPAAGPGTPAKEKSPAETATSGAAKPAAKKAVPSSQ 372
>gnl|CDD|215598 PLN03138, PLN03138, Protein TOC75; Provisional.
Length = 796
Score = 28.7 bits (64), Expect = 3.9
Identities = 15/57 (26%), Positives = 21/57 (36%)
Query: 111 QEKALKNTTGGAGGGGSGTGSGSGSAGGAASKSKRGRKKAKDKAESATDAAGDDKSS 167
L + GGGG G G G GG G + + + DA D++ S
Sbjct: 67 AVALLSASAISGGGGGGGGGFGGFGGGGGGGGGGGGGWRFWLRLFAPADAHADEEQS 123
>gnl|CDD|218602 pfam05478, Prominin, Prominin. The prominins are an emerging
family of proteins that among the multispan membrane
proteins display a novel topology. Mouse prominin and
human prominin (mouse)-like 1 (PROML1) are predicted to
contain five membrane spanning domains, with an
N-terminal domain exposed to the extracellular space
followed by four, alternating small cytoplasmic and
large extracellular, loops and a cytoplasmic C-terminal
domain. The exact function of prominin is unknown
although in humans defects in PROM1, the gene coding for
prominin, cause retinal degeneration.
Length = 807
Score = 28.4 bits (64), Expect = 4.0
Identities = 12/73 (16%), Positives = 28/73 (38%), Gaps = 16/73 (21%)
Query: 10 LDSLDSLPIELQRNFT-----LMRELDSR-------AQDVMKTIDRVAEDYLDNMKHYSK 57
+ + +P +++ + + LDS A+D+ + V L+N + S
Sbjct: 342 NSTFEEIPSKVKNQTSSVVPDVKAALDSLGTDIKSVAEDLPLQVLSVLSQILNNTQSSSN 401
Query: 58 DKKKETLAEIQKY 70
L +++Y
Sbjct: 402 PY----LPYVEQY 410
>gnl|CDD|233028 TIGR00571, dam, DNA adenine methylase (dam). All proteins in this
family for which functions are known are DNA-adenine
methyltransferases. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University). The DNA adenine methylase (dam) of
E. coli and related species is instrumental in
distinguishing the newly synthesized strand during DNA
replication for methylation-directed mismatch repair.
This family includes several phage methylases and a
number of different restriction enzyme chromosomal
site-specific modification systems [DNA metabolism, DNA
replication, recombination, and repair].
Length = 266
Score = 28.1 bits (63), Expect = 4.4
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 41 IDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKE 76
+ V E LD K Y+++ KE E+++ F+K+ E
Sbjct: 65 KNNVDELILDVRKLYAEENTKEYYYEVREDFNKSTE 100
>gnl|CDD|215278 PLN02502, PLN02502, lysyl-tRNA synthetase.
Length = 553
Score = 28.4 bits (64), Expect = 4.4
Identities = 12/49 (24%), Positives = 19/49 (38%)
Query: 126 GSGTGSGSGSAGGAASKSKRGRKKAKDKAESATDAAGDDKSSNSKKKVA 174
S S +A K+K+ ++ K E+ AA S+K A
Sbjct: 2 ESNGEPLSKNALKKRLKAKQAEEEKAAKEEAKAAAAAAAAKGRSRKSAA 50
>gnl|CDD|151621 pfam11179, DUF2967, Protein of unknown function (DUF2967). This
family of proteins with unknown function appears to be
restricted to Drosophila.
Length = 284
Score = 28.0 bits (61), Expect = 4.6
Identities = 19/65 (29%), Positives = 25/65 (38%)
Query: 113 KALKNTTGGAGGGGSGTGSGSGSAGGAASKSKRGRKKAKDKAESATDAAGDDKSSNSKKK 172
K N G SG G+GSG+ G S G A A D A D + ++
Sbjct: 38 KNYGNEDAKDAGRASGKGTGSGAGVGGGGGSGSGVGGNGVMAAGAADEAADAQEEDAIAN 97
Query: 173 VAKKI 177
KK+
Sbjct: 98 RNKKL 102
>gnl|CDD|221526 pfam12316, Dsh_C, Segment polarity protein dishevelled (Dsh) C
terminal. This domain family is found in eukaryotes,
and is typically between 177 and 207 amino acids in
length. The family is found in association with
pfam00778, pfam02377, pfam00610, pfam00595. The segment
polarity gene dishevelled (dsh) is required for pattern
formation of the embryonic segments. It is involved in
the determination of body organisation through the
Wingless pathway (analogous to the Wnt-1 pathway).
Length = 202
Score = 27.6 bits (61), Expect = 5.2
Identities = 14/48 (29%), Positives = 20/48 (41%), Gaps = 6/48 (12%)
Query: 122 AGGGGSGTGSGSGSAGGAASKSKRGRKKAKDKAESATDAAGDDKSSNS 169
G G +G+ GS +++S R +A D E G KS S
Sbjct: 61 YGSGSAGSQHSEGSRSSGSNRSDGERSRAADGRE------GGRKSGGS 102
>gnl|CDD|217348 pfam03064, U79_P34, HSV U79 / HCMV P34. This family represents
herpes virus protein U79 and cytomegalovirus early
phosphoprotein P34 (UL112).
Length = 238
Score = 27.9 bits (62), Expect = 5.4
Identities = 18/94 (19%), Positives = 33/94 (35%), Gaps = 4/94 (4%)
Query: 59 KKKETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQEKALKNT 118
K E + + + K + + + Q + + +K D ++ QE+ +N
Sbjct: 138 KNAEKFEKECRALSRKKSDDEHRKRSGKQKEKRRVEDSQKHKED----RRKKQEEKRRND 193
Query: 119 TGGAGGGGSGTGSGSGSAGGAASKSKRGRKKAKD 152
GGG G+ G K R+K D
Sbjct: 194 EDKRPGGGGGSSGGQSGLSTKDEPPKEKRQKHHD 227
>gnl|CDD|215521 PLN02967, PLN02967, kinase.
Length = 581
Score = 28.1 bits (62), Expect = 5.4
Identities = 12/42 (28%), Positives = 19/42 (45%), Gaps = 5/42 (11%)
Query: 135 SAGGAASKSKRGRKKAKDKAESATDAAGDDKSSNSKKKVAKK 176
+A SK R + K A A+ D + ++KKV K+
Sbjct: 104 AALDKESKKTPRRTRRK-----AAAASSDVEEEKTEKKVRKR 140
>gnl|CDD|235782 PRK06341, PRK06341, single-stranded DNA-binding protein;
Provisional.
Length = 166
Score = 27.5 bits (61), Expect = 5.4
Identities = 11/33 (33%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 116 KNTTGGAGGGGSGTGSGS-GSAGGAASKSKRGR 147
+ GG GGGG G G GS+G + +
Sbjct: 117 RGEGGGGGGGGDDGGGGDFGSSGPSRGGPRPAS 149
Score = 27.5 bits (61), Expect = 6.1
Identities = 14/45 (31%), Positives = 18/45 (40%)
Query: 120 GGAGGGGSGTGSGSGSAGGAASKSKRGRKKAKDKAESATDAAGDD 164
G GGGG G G G G++ S+ G + A DD
Sbjct: 118 GEGGGGGGGGDDGGGGDFGSSGPSRGGPRPASSGGGGNFSRDMDD 162
>gnl|CDD|187662 cd09761, A3DFK9-like_SDR_c, Clostridium thermocellum A3DFK9-like, a
putative carbohydrate or polyalcohol metabolizing SDR,
classical (c) SDRs. This subgroup includes a putative
carbohydrate or polyalcohol metabolizing SDR (A3DFK9)
from Clostridium thermocellum. Its members have a
TGXXXGXG classical-SDR glycine-rich NAD-binding motif,
and some have a canonical SDR active site tetrad (A3DFK9
lacks the upstream Asn). SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH
numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 242
Score = 27.5 bits (61), Expect = 5.6
Identities = 20/81 (24%), Positives = 27/81 (33%), Gaps = 6/81 (7%)
Query: 119 TGGAGGGGSGTGSGSGSAGG----AASKSKRGRKKAKDKAESATDAAGDDKSSNSKKKVA 174
TGG G G AG A +RG A+ + + GD K V
Sbjct: 7 TGGGHGIGKQICLDFLEAGDKVVFADIDEERGADFAEAEGPNLFFVHGDVADETLVKFVV 66
Query: 175 KKITGVGGVVGVL--NAIVAA 193
+ G + VL NA +
Sbjct: 67 YAMLEKLGRIDVLVNNAARGS 87
>gnl|CDD|222425 pfam13865, FoP_duplication, C-terminal duplication domain of Friend
of PRMT1. Fop, or Friend of Prmt1, proteins are
conserved from fungi and plants to vertebrates. There is
little that is actually conserved except for this
C-terminal LDXXLDAYM region where X is any amino acid).
The Fop proteins themselves are nuclear proteins
localised to regions with low levels of DAPI, with a
punctate/speckle-like distribution. Fop is a
chromatin-associated protein and it colocalises with
facultative heterochromatin. It is is critical for
oestrogen-dependent gene activation.
Length = 76
Score = 26.3 bits (58), Expect = 5.6
Identities = 15/60 (25%), Positives = 19/60 (31%), Gaps = 6/60 (10%)
Query: 119 TGGAGGGGSGTGSGSGSAGGAASKSKRGRKKA--KDKAESAT----DAAGDDKSSNSKKK 172
G G G A + + GRK K + T DA D S +K K
Sbjct: 2 GGRKGSRGGKFRPRGRGARRGRRRGRGGRKGKGGAAKPKPKTREDLDAELDQYMSTTKSK 61
>gnl|CDD|221857 pfam12923, RRP7, Ribosomal RNA-processing protein 7 (RRP7). RRP7
is an essential protein in yeast that is involved in
pre-rRNA processing and ribosome assembly. It is
speculated to be required for correct assembly of rpS27
into the pre-ribosomal particle.
Length = 131
Score = 27.2 bits (61), Expect = 5.8
Identities = 18/66 (27%), Positives = 27/66 (40%), Gaps = 4/66 (6%)
Query: 90 EMVDKYIRKLDTDLARFEQEIQEKALKN----TTGGAGGGGSGTGSGSGSAGGAASKSKR 145
E VD Y+ K D ++E + ++ + TT GG G+ A K K
Sbjct: 21 EEVDTYMEKYDKREEEAKEEAKARSEPDEDGWTTVTRGGRKRKAGASRNKAAEERRKLKE 80
Query: 146 GRKKAK 151
+KK K
Sbjct: 81 KKKKKK 86
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 28.0 bits (63), Expect = 5.8
Identities = 13/88 (14%), Positives = 33/88 (37%), Gaps = 11/88 (12%)
Query: 28 RELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKVQLAIQ 87
R+L S + + +D+ ++ Y + + +E D + +
Sbjct: 46 RKLRSLLTKLSEALDK--------LRSYLPKLNPLREEKKKVSVKSLEELIKDVEEELEK 97
Query: 88 TYEMVDKY---IRKLDTDLARFEQEIQE 112
+ + + I +L+ ++ EQEI+
Sbjct: 98 IEKEIKELEEEISELENEIKELEQEIER 125
>gnl|CDD|236172 PRK08173, PRK08173, DNA topoisomerase III; Validated.
Length = 862
Score = 28.1 bits (63), Expect = 6.3
Identities = 12/43 (27%), Positives = 17/43 (39%)
Query: 136 AGGAASKSKRGRKKAKDKAESATDAAGDDKSSNSKKKVAKKIT 178
A A + + A KAE A K + +KK A+K
Sbjct: 820 AAAAKKTAAKATAAAATKAEKAAAKKAPAKKTAAKKTAARKTG 862
>gnl|CDD|188995 cd06456, M3A_DCP, Peptidase family M3 dipeptidyl carboxypeptidase
(DCP). Peptidase family M3 dipeptidyl carboxypeptidase
(DCP; Dcp II; peptidyl dipeptidase; EC 3.4.15.5). This
metal-binding M3A family also includes oligopeptidase A
(OpdA; EC 3.4.24.70) enzyme. DCP cleaves dipeptides off
the C-termini of various peptides and proteins, the
smallest substrate being N-blocked tripeptides and
unblocked tetrapeptides. DCP from E. coli is inhibited
by the anti-hypertensive drug captopril, an inhibitor of
the mammalian angiotensin converting enzyme (ACE, also
called peptidyl dipeptidase A). Oligopeptidase A (OpdA)
may play a specific role in the degradation of signal
peptides after they are released from precursor forms of
secreted proteins. It can also cleave N-acetyl-L-Ala.
Length = 654
Score = 27.8 bits (63), Expect = 6.4
Identities = 15/45 (33%), Positives = 28/45 (62%), Gaps = 3/45 (6%)
Query: 39 KTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKVQ 83
KT + V +L+++ +K + K+ LAE+Q + +E GDD++Q
Sbjct: 267 KTPEAV-LAFLEDLAEKAKPQAKKELAELQAFAK--EEGGDDELQ 308
>gnl|CDD|236312 PRK08617, PRK08617, acetolactate synthase; Reviewed.
Length = 552
Score = 27.9 bits (63), Expect = 6.6
Identities = 20/91 (21%), Positives = 39/91 (42%), Gaps = 9/91 (9%)
Query: 13 LDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKK-KETLAEIQKYF 71
+D LP E+ + REL D+ T+D +AE + S + E L E++
Sbjct: 298 IDVLPAEIDNYYQPEREL---IGDIAATLDLLAEK----LDGLSLSPQSLEILEELRAQL 350
Query: 72 DKTKEYGDDKVQLAIQTYEMVDKYIRKLDTD 102
++ E + A+ ++ ++ + TD
Sbjct: 351 EELAERPARLEEGAVHPLRIIRA-LQDIVTD 380
>gnl|CDD|235082 PRK02888, PRK02888, nitrous-oxide reductase; Validated.
Length = 635
Score = 27.6 bits (62), Expect = 6.7
Identities = 10/57 (17%), Positives = 16/57 (28%)
Query: 107 EQEIQEKALKNTTGGAGGGGSGTGSGSGSAGGAASKSKRGRKKAKDKAESATDAAGD 163
+ + T AG G+ +G AA + A A G+
Sbjct: 6 PSGLSRRQFLGTAALAGAAGAAGSTGLLGGALAAGAAAAAAAAAAAAGGKYEVAPGE 62
>gnl|CDD|220369 pfam09731, Mitofilin, Mitochondrial inner membrane protein.
Mitofilin controls mitochondrial cristae morphology.
Mitofilin is enriched in the narrow space between the
inner boundary and the outer membranes, where it forms a
homotypic interaction and assembles into a large
multimeric protein complex. The first 78 amino acids
contain a typical amino-terminal-cleavable mitochondrial
presequence rich in positive-charged and hydroxylated
residues and a membrane anchor domain. In addition, it
has three centrally located coiled coil domains.
Length = 493
Score = 27.7 bits (62), Expect = 6.7
Identities = 24/113 (21%), Positives = 46/113 (40%), Gaps = 26/113 (23%)
Query: 10 LDSLDSLPIELQRNFTLMRELDSRAQDVMK-----TIDRVAEDYLDNMKHYSKDKKKETL 64
+ LD L +L L E + + +K + ++ E+ L ++ K+
Sbjct: 169 KEELDQLSKKLAE---LKAEEEEELERALKEKREELLSKLEEELLARLES----KEAALE 221
Query: 65 AEIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQEKALKN 117
+++ F++ KE E+ KY KL +L R + ++K LKN
Sbjct: 222 KQLRLEFEREKE-------------ELRKKYEEKLRQELERQAEAHEQK-LKN 260
>gnl|CDD|190954 pfam04360, Serglycin, Serglycin. Serglycin is the most prevalent
proteoglycan produced in haemopoietic cells. Serglycin
is a proteinase resistant secretory granule
proteoglycan.
Length = 150
Score = 26.8 bits (59), Expect = 6.9
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 124 GGGSGTGSGSGSAGGAAS 141
G GSG+GSGSGS G+
Sbjct: 93 GSGSGSGSGSGSGSGSGF 110
Score = 26.8 bits (59), Expect = 7.3
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 119 TGGAGGGGSGTGSGSGS 135
+G G GSG+GSGSGS
Sbjct: 92 SGSGSGSGSGSGSGSGS 108
>gnl|CDD|233909 TIGR02520, pilus_B_mal_scr, type IVB pilus formation outer membrane
protein, R64 PilN family. Several related protein
families encode outer membrane pore proteins for type II
secretion, type III secretion, and type IV pilus
formation. This protein family appears to encode a
secretin for pilus formation, although it is quite
different from PilQ. Members include the PilN
lipoprotein of the plasmid R64 thin pilus, a type IV
pilus. Scoring between the trusted and noise cutoffs are
examples of bundle-forming pilus B (bfpB) [Cell
envelope, Surface structures, Protein fate, Protein and
peptide secretion and trafficking].
Length = 497
Score = 27.5 bits (61), Expect = 6.9
Identities = 10/28 (35%), Positives = 13/28 (46%)
Query: 118 TTGGAGGGGSGTGSGSGSAGGAASKSKR 145
+T G+G SG SGS A K +
Sbjct: 178 STAGSGSSSSGGSGNSGSTQSTAVKLES 205
>gnl|CDD|226903 COG4520, LipA, Surface antigen [Cell envelope biogenesis, outer
membrane].
Length = 136
Score = 26.7 bits (59), Expect = 7.0
Identities = 9/27 (33%), Positives = 12/27 (44%)
Query: 117 NTTGGAGGGGSGTGSGSGSAGGAASKS 143
TT G G GG+ G+ + G S
Sbjct: 9 TTTSGGGAGGALAGAQAIPTKGCRSTV 35
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 27.7 bits (62), Expect = 7.1
Identities = 14/85 (16%), Positives = 43/85 (50%), Gaps = 6/85 (7%)
Query: 28 RELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDDKVQLAIQ 87
EL+ ++ ++ +D + ++ ++ ++++K AE +Y KE + + ++
Sbjct: 177 EELE-EVEENIERLDLIIDEKRQQLERLRREREK---AE--RYQALLKEKREYEGYELLK 230
Query: 88 TYEMVDKYIRKLDTDLARFEQEIQE 112
E +++ ++ LA E+E+++
Sbjct: 231 EKEALERQKEAIERQLASLEEELEK 255
>gnl|CDD|237654 PRK14278, PRK14278, chaperone protein DnaJ; Provisional.
Length = 378
Score = 27.7 bits (62), Expect = 7.2
Identities = 16/35 (45%), Positives = 17/35 (48%), Gaps = 7/35 (20%)
Query: 120 GGAGGGGSGTGSGSGS-------AGGAASKSKRGR 147
G GGGG G G G GGAAS+ RGR
Sbjct: 74 AGGGGGGFGGGFGGLGDVFEAFFGGGAASRGPRGR 108
>gnl|CDD|222127 pfam13436, Gly-zipper_OmpA, Glycine-zipper containing OmpA-like
membrane domain.
Length = 116
Score = 26.5 bits (59), Expect = 7.2
Identities = 9/32 (28%), Positives = 15/32 (46%)
Query: 119 TGGAGGGGSGTGSGSGSAGGAASKSKRGRKKA 150
G A G G +G+GS ++ ++R A
Sbjct: 77 IGAAAGALVGAAAGAGSGQYSSYGAQRRYDNA 108
Score = 26.5 bits (59), Expect = 8.3
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 121 GAGGGGSGTGSGSGSAGGAASKSKRGR 147
G GG G+ G+ +G+ GAA+ + G+
Sbjct: 69 GGGGDGAAIGAAAGALVGAAAGAGSGQ 95
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
Length = 509
Score = 27.7 bits (62), Expect = 7.3
Identities = 10/76 (13%), Positives = 20/76 (26%), Gaps = 2/76 (2%)
Query: 101 TDLARFEQEIQEKALKNTTGGAGGGGSGTGSGSGSAGGAASKSKRGRKKAKDKAESATDA 160
++ + ++ + G + + K + KA A
Sbjct: 36 EEIKEALESKKKTPEQIDQVLIFLSGMVKDTDDATESDIPKKKTKTAAKAAAAKAPAKKK 95
Query: 161 AGDDKSSNSKKKVAKK 176
+S KK KK
Sbjct: 96 L--KDELDSSKKAEKK 109
>gnl|CDD|204345 pfam09932, DUF2164, Uncharacterized conserved protein (DUF2164).
This domain, found in various hypothetical prokaryotic
proteins, has no known function.
Length = 76
Score = 25.6 bits (57), Expect = 7.5
Identities = 9/17 (52%), Positives = 16/17 (94%)
Query: 56 SKDKKKETLAEIQKYFD 72
SK++K+E +A+IQ+YF+
Sbjct: 4 SKEQKQELVAKIQRYFE 20
>gnl|CDD|214018 cd12925, iSH2_PIK3R3, Inter-Src homology 2 (iSH2) helical domain of
Class IA Phosphoinositide 3-kinase Regulatory subunit 3,
PIK3R3, also called p55gamma. PI3Ks catalyze the
transfer of the gamma-phosphoryl group from ATP to the
3-hydroxyl of the inositol ring of
D-myo-phosphatidylinositol (PtdIns) or its derivatives.
They play an important role in a variety of fundamental
cellular processes, including cell motility, the Ras
pathway, vesicle trafficking and secretion, immune cell
activation, and apoptosis. They are classified according
to their substrate specificity, regulation, and domain
structure. Class IA PI3Ks are heterodimers of a p110
catalytic (C) subunit and a p85-related regulatory (R)
subunit. The R subunit down-regulates PI3K basal
activity, stabilizes the C subunit, and plays a role in
the activation downstream of tyrosine kinases. All R
subunits contain two SH2 domains that flank an
intervening helical domain (iSH2), which binds to the
N-terminal adaptor-binding domain (ABD) of the catalytic
subunit. p55gamma, also called PIK3R3 or p55PIK, also
contains a unique N-terminal 24-amino acid residue (N24)
that interacts with cell cycle modulators to promote
cell cycle progression.
Length = 161
Score = 26.9 bits (59), Expect = 7.5
Identities = 27/124 (21%), Positives = 57/124 (45%), Gaps = 24/124 (19%)
Query: 11 DSLDSLPIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLD-----NMKHYSKDKKKETLA 65
D++D++ +LQ E S+ Q+ K DR+ E+Y MK + + ET+
Sbjct: 1 DNIDAVGRKLQ-------EYHSQYQEKSKEYDRLYEEYTKTSQEIQMKRTAIEAFNETIK 53
Query: 66 EIQK-----------YFDKTKEYGDDK-VQLAIQTYEMVDKYIRKLDTDLARFEQEIQEK 113
++ Y ++ + G++K ++ + YE + + ++ R EQ+++ +
Sbjct: 54 IFEEQCHTQERYSKEYIERFRREGNEKEIERIMMNYEKLKSRLGEIHDSKMRLEQDLKTQ 113
Query: 114 ALKN 117
AL N
Sbjct: 114 ALDN 117
>gnl|CDD|147458 pfam05268, GP38, Phage tail fibre adhesin Gp38. This family
contains several Gp38 proteins from T-even-like phages.
Gp38, together with a second phage protein, gp57,
catalyzes the organisation of gp37 but is absent from
the phage particle. Gp37 is responsible for receptor
recognition.
Length = 261
Score = 27.5 bits (61), Expect = 7.6
Identities = 15/35 (42%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 115 LKNTTGGAGGG---GSGTGSGSGSAGGAASKSKRG 146
N G GGG G+G SGS +GG AS + G
Sbjct: 168 RGNGVCGGGGGRPFGAGGKSGSHMSGGNASLTAPG 202
>gnl|CDD|147982 pfam06112, Herpes_capsid, Gammaherpesvirus capsid protein. This
family consists of several Gammaherpesvirus capsid
proteins. The exact function of this family is unknown.
Length = 148
Score = 26.7 bits (59), Expect = 7.8
Identities = 17/50 (34%), Positives = 22/50 (44%), Gaps = 12/50 (24%)
Query: 124 GGGSGTGSGSGSAGGAASKSKRGRKKAKDKAESATDA-AGDDKSSNSKKK 172
G SG+ SG ++S S S + A AGD S+SKKK
Sbjct: 110 SGSSGSALSSGPGSLSSSSS-----------LSGSGAGAGDTAPSSSKKK 148
>gnl|CDD|238288 cd00520, RRF, Ribosome recycling factor (RRF). Ribosome recycling
factor dissociates the posttermination complex, composed
of the ribosome, deacylated tRNA, and mRNA, after
termination of translation. Thus ribosomes are
"recycled" and ready for another round of protein
synthesis. RRF is believed to bind the ribosome at the
A-site in a manner that mimics tRNA, but the specific
mechanisms remain unclear. RRF is essential for
bacterial growth. It is not necessary for cell growth
in archaea or eukaryotes, but is found in mitochondria
or chloroplasts of some eukaryotic species.
Length = 179
Score = 26.8 bits (60), Expect = 7.9
Identities = 20/81 (24%), Positives = 42/81 (51%), Gaps = 10/81 (12%)
Query: 33 RAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKEYGDD---KVQLAIQTY 89
R ++++K ++AE+ +++ +D + K +K KE +D K + +Q
Sbjct: 105 RRKELVKDAKKIAEEAKVAIRNIRRDANDKI-----KKLEKEKEISEDEVKKAEEDLQK- 158
Query: 90 EMVDKYIRKLDTDLARFEQEI 110
+ D+YI+K+D L E+E+
Sbjct: 159 -LTDEYIKKIDELLKSKEKEL 178
>gnl|CDD|183745 PRK12787, fliX, flagellar assembly regulator FliX; Reviewed.
Length = 138
Score = 26.5 bits (59), Expect = 8.0
Identities = 10/43 (23%), Positives = 15/43 (34%), Gaps = 5/43 (11%)
Query: 120 GGAGGGGSGTGSGSGSAGGAASKSKRGRKKAKDKAESATDAAG 162
G G + GS S G++ G + A A +A
Sbjct: 4 YGPNGTTAAGGSRSARRTGSS-----GFSLPDESASGAGEARA 41
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 27.5 bits (61), Expect = 8.1
Identities = 10/55 (18%), Positives = 18/55 (32%)
Query: 97 RKLDTDLARFEQEIQEKALKNTTGGAGGGGSGTGSGSGSAGGAASKSKRGRKKAK 151
R+ DT + E+E QE + + + S G + K +
Sbjct: 978 RRCDTLIRLIEKENQEYDERERQARKEKKLAKNATPSKRPSGRQANESPSSLKKR 1032
>gnl|CDD|219366 pfam07295, DUF1451, Protein of unknown function (DUF1451). This
family consists of several hypothetical bacterial
proteins of around 160 residues in length. Members of
this family contain four highly conserved cysteine
resides toward the C-terminal region of the protein. The
function of this family is unknown.
Length = 148
Score = 26.8 bits (60), Expect = 8.2
Identities = 12/61 (19%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 52 MKHYSKDKKKETLAEIQKYFDKTKEYGDDKVQLAIQTYEMVDKYIRKLDTDLARFEQEIQ 111
+ ++ K T E+++ ++ KEY +L + ++ Y+++ DL F + +
Sbjct: 1 VLDRLSERLKHTEKELKEAIEQAKEYLQAAEELTREELALIGAYLKR---DLEEFLRSYE 57
Query: 112 E 112
E
Sbjct: 58 E 58
>gnl|CDD|173607 PTZ00417, PTZ00417, lysine-tRNA ligase; Provisional.
Length = 585
Score = 27.7 bits (61), Expect = 8.4
Identities = 31/117 (26%), Positives = 47/117 (40%), Gaps = 29/117 (24%)
Query: 17 PIELQRNFTLMRELDSRAQDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQK--YFDKT 74
P+ ++ F M E + + VM+ +V SKDKKKE AE+ Y++
Sbjct: 39 PVHCKQCFVTMSE---KKEHVMEGEKKVR------SVQASKDKKKEEEAEVDPRLYYENR 89
Query: 75 KEYGDDKVQLAIQTY-----------EMVDKYIRKLDTDLARFEQEIQEKALKNTTG 120
++ ++ I Y E V+KY DLA E E + N TG
Sbjct: 90 SKFIQEQKAKGINPYPHKFERTITVPEFVEKY-----QDLASGEH--LEDTILNVTG 139
>gnl|CDD|236382 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau;
Validated.
Length = 598
Score = 27.6 bits (62), Expect = 8.5
Identities = 8/30 (26%), Positives = 12/30 (40%)
Query: 112 EKALKNTTGGAGGGGSGTGSGSGSAGGAAS 141
++AL+ G G G G G G +
Sbjct: 381 DEALRRLQEGPPSPGGGGGGPPGGGGAPGA 410
>gnl|CDD|176238 cd08277, liver_alcohol_DH_like, Liver alcohol dehydrogenase.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. There are 7 vertebrate ADH 7
classes, 6 of which have been identified in humans.
Class III, glutathione-dependent formaldehyde
dehydrogenase, has been identified as the primordial
form and exists in diverse species, including plants,
micro-organisms, vertebrates, and invertebrates. Class
I, typified by liver dehydrogenase, is an evolving
form. Gene duplication and functional specialization of
ADH into ADH classes and subclasses created numerous
forms in vertebrates. For example, the A, B and C
(formerly alpha, beta, gamma) human class I subunits
have high overall structural similarity, but differ in
the substrate binding pocket and therefore in substrate
specificity. In human ADH catalysis, the zinc ion helps
coordinate the alcohol, followed by deprotonation of a
histidine (His-51), the ribose of NAD, a serine
(Ser-48) , then the alcohol, which allows the transfer
of a hydride to NAD+, creating NADH and a zinc-bound
aldehyde or ketone. In yeast and some bacteria, the
active site zinc binds an aldehyde, polarizing it, and
leading to the reverse reaction. ADH is a member of the
medium chain alcohol dehydrogenase family (MDR), which
has a NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a catalytic
zinc at the active site and a structural zinc in a lobe
of the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 365
Score = 27.3 bits (61), Expect = 8.6
Identities = 21/85 (24%), Positives = 31/85 (36%), Gaps = 14/85 (16%)
Query: 121 GAGGGGSGTGSGSGSAGGAASK----SKRGRKKAKDKAESATDAAGDDKSSNSKKKVAKK 176
G G G G+ AG AS+ K K K ATD S +V ++
Sbjct: 192 GLGAVGLSAIMGAKIAG--ASRIIGVDINEDKFEKAKEFGATDFINPKDSDKPVSEVIRE 249
Query: 177 ITGVG--------GVVGVLNAIVAA 193
+TG G G ++N + +
Sbjct: 250 MTGGGVDYSFECTGNADLMNEALES 274
>gnl|CDD|191367 pfam05761, 5_nucleotid, 5' nucleotidase family. This family of
eukaryotic proteins includes 5' nucleotidase enzymes,
such as purine 5'-nucleotidase EC:3.1.3.5.
Length = 448
Score = 27.2 bits (61), Expect = 8.9
Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 9/42 (21%)
Query: 35 QDVMKTIDRVAEDYLDNMKHYSKDKKKETLAEIQKYFDKTKE 76
QDV ID V H K+E L ++++Y K E
Sbjct: 155 QDVRDAIDDV---------HRDGSLKREVLEDLERYVIKDPE 187
>gnl|CDD|199210 cd02258, Peptidase_C25_N, Peptidase C25 family N-terminal domain,
found in Arg-gingipain (Rgp), Lys-gingipain (Kgp) and
related proteins. Peptidase family C25 is a unique
class of cysteine proteases, exemplified by gingipain,
which is produced by Porphyromonas gingivalis. P.
gingivalis is one of the primary gram-negative pathogens
that causes periodontitis, a disease that is also
associated with other diseases such as diabetes and
cardiovascular disease. Gingipains are a group of
extracellular Arg- and Lys-specific proteinases called
Arg-gingipain (Rgp) and Lys-gingipain (Kgp); RgpA and
RgpB are homologous Arg-specific gingipains encoded by
two closely related genes, rgpA and rgpB, while
Lys-specific gingipain is encoded by the single kgp
gene. Mutant studies have shown that, among the large
quantities of proteolytic enzymes produced by P.
gingivalis, these three proteases are major virulence
factors of this bacterium. All three genes encode an
N-terminal pre-pro fragment, followed by the protease
domain; however, rgpA and kgp also encode additional
C-terminal HA (hemaglutinin/adhesion) subunits which
consist of several sequence-related adhesion domains.
Although unique, their cysteine protease active site
residues (His and Cys) forming the catalytic dyad are
well-conserved, cleaving the C-terminal peptide bond
with Arg or Lys residues. Gingipains are evolutionarily
related to other highly specific proteases including
caspases, clostripain, legumains, and separase.
Gingipains function by dysregulating host defense and
inflammatory responses, and degrading host proteins,
e.g. tissue, cells, matrix, plasma and immunological
proteins. They are proposed to enhance gingival
crevicular fluid (GCF) production through activation of
the kallikrein/kinin pathways, thus increasing vascular
permeability and causing gingival inflammation, a
distinctive feature of periodontitis. RgpA and RgpB are
also able to cleave and activate coagulation factors IX
and X in order to activate prothrombin to produce
thrombin, which in turn increases production of GCF. The
gingipains also play a pivotal role in the survival of
P. gingivalis in the host by attacking the host defense
system through cleavage of several immunological
molecules, while at the same time evading the
host-immune response by dysregulating the cytokine
network.
Length = 382
Score = 27.3 bits (61), Expect = 9.1
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 62 ETLAEIQKYFDKTKEYGDDK 81
+T AE + Y DK Y ++K
Sbjct: 149 KTNAEAKNYVDKIIAYENNK 168
>gnl|CDD|236799 PRK10930, PRK10930, FtsH protease regulator HflK; Provisional.
Length = 419
Score = 27.5 bits (61), Expect = 9.2
Identities = 13/27 (48%), Positives = 14/27 (51%)
Query: 121 GAGGGGSGTGSGSGSAGGAASKSKRGR 147
G GGG GTGSG GS+ GR
Sbjct: 53 GGLGGGKGTGSGGGSSSQGPRPQLGGR 79
>gnl|CDD|218598 pfam05470, eIF-3c_N, Eukaryotic translation initiation factor 3
subunit 8 N-terminus. The largest of the mammalian
translation initiation factors, eIF3, consists of at
least eight subunits ranging in mass from 35 to 170 kDa.
eIF3 binds to the 40 S ribosome in an early step of
translation initiation and promotes the binding of
methionyl-tRNAi and mRNA.
Length = 593
Score = 27.5 bits (61), Expect = 9.2
Identities = 18/110 (16%), Positives = 35/110 (31%), Gaps = 9/110 (8%)
Query: 92 VDKYIRKLDTDLARF----EQEIQEKALKNTTGGAGGGGSGTGSGSGSAGGAASKSKRGR 147
V K ++ + D+ R+ E E +E+ G A + S
Sbjct: 117 VKKNNKQFEDDITRYREDPESEDEEEEEDEDDDDDGSDDEDEDEDGVGATEEVAASSESG 176
Query: 148 KKAKDKAESATDAAGDDKSSNSKKKVA----KKITGVGGVVGVLNAIVAA 193
+ + + A K ++ ++IT V L I++A
Sbjct: 177 VDRVKEDDEEDEDADLSKKDVLEEPKMFKKPEEIT-WDDVFKKLKEIMSA 225
>gnl|CDD|236957 PRK11700, PRK11700, hypothetical protein; Provisional.
Length = 187
Score = 26.7 bits (60), Expect = 9.4
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 99 LDTDLARFEQEIQE 112
L DL RFEQ+IQE
Sbjct: 13 LLADLPRFEQKIQE 26
>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional.
Length = 333
Score = 27.2 bits (60), Expect = 9.8
Identities = 14/53 (26%), Positives = 21/53 (39%), Gaps = 2/53 (3%)
Query: 127 SGTGSGSGSAGGAASKSKRGRKKAKDKAESATDAAGDDKSSNSKKKVAKKITG 179
+ G+ + +K G KKA KA+SA K +K V+ K
Sbjct: 192 AAVGAANAKKAAKTPAAKSGAKKASAKAKSAAKKVS--KKKAAKTAVSAKKAA 242
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
0.312 0.130 0.377
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,993,730
Number of extensions: 1240604
Number of successful extensions: 2520
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2263
Number of HSP's successfully gapped: 216
Length of query: 259
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 164
Effective length of database: 6,723,972
Effective search space: 1102731408
Effective search space used: 1102731408
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 58 (26.1 bits)