RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15222
(444 letters)
>gnl|CDD|235551 PRK05667, dnaG, DNA primase; Validated.
Length = 580
Score = 350 bits (900), Expect = e-115
Identities = 136/366 (37%), Positives = 194/366 (53%), Gaps = 30/366 (8%)
Query: 4 ASDFYKIQL--KNSKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLDYN-NINTL 60
A+ FY+ QL EA +L KRGL+EE I RF +GYAP+ W+AL K + L
Sbjct: 117 AAKFYQQQLRTPEGAEARQYLYKRGLSEETIERFGIGYAPDGWDALLKHLGGKGFSEKEL 176
Query: 61 ASSGLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKY 120
+GL++ + YDRFR RIMFPI++ G++IGFGGR++ D + KY
Sbjct: 177 EEAGLLIKNE----------DGGGPYDRFRNRIMFPIRDLRGRVIGFGGRVLGDD-KPKY 225
Query: 121 INSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACT 180
+NSPETPLFHK LYGL EA+ AI K V++ EGYMDVI L Q G VA LGTA T
Sbjct: 226 LNSPETPLFHKGRVLYGLDEARKAIAKKKQVIVVEGYMDVIALHQAGITNAVASLGTALT 285
Query: 181 STHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYI 240
H+K + T+ +I FDGD+AGR+AA RALE+ L D + ++ FLPD DPD +
Sbjct: 286 EEHLKLLRRLTDEVILCFDGDKAGRKAALRALELALPLLKDGRQVRVAFLPDGKDPDDLV 345
Query: 241 RKFGYKIFSKKVLEAMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPL-----S 295
RK G + F + +A+ L +F + +I +L T + L + PL
Sbjct: 346 RKEGPEAFRALLEQAIPLSEFLIRRLIPGKDLDTPEG------RAALLERAAPLIAKIPD 399
Query: 296 SSLRFKIISSLSKIIKVSFNEINNLFKINTSSIKHKTIEKKNIQPICIEYQIMKLLISYP 355
+LR L++ + + + + K +P E +++ LL+ +P
Sbjct: 400 PTLRDSYRRKLAERLGILDDAQLEQLVPKAQEPQ-----LKAERPRTAERELLALLLQHP 454
Query: 356 SLINEI 361
L E+
Sbjct: 455 ELAEEV 460
>gnl|CDD|233392 TIGR01391, dnaG, DNA primase, catalytic core. Members of this
family are DNA primase, a ubiquitous bacteria protein.
Most members of this family contain nearly two hundred
additional residues C-terminal to the region represented
here, but conservation between species is poor and the
C-terminal region was not included in the seed
alignment. This protein contains a CHC2 zinc finger
(pfam01807) and a Toprim domain (pfam01751) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 415
Score = 273 bits (700), Expect = 8e-88
Identities = 130/299 (43%), Positives = 177/299 (59%), Gaps = 23/299 (7%)
Query: 4 ASDFYKIQLKNSKE---AINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLDYNNINT- 59
A+ F+K QLK++ E A+++L+ RGL++E I RF LGYAPN W+ L + +
Sbjct: 120 AAKFFKNQLKHTPENRAALDYLQSRGLSDETIDRFELGYAPNNWDFLFDFLQNKKGFDLE 179
Query: 60 -LASSGLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEA 118
LA +GL+V K E K YDRFR RIMFPI + G+++GFGGR + D +
Sbjct: 180 LLAEAGLLVKK-----------ENGKYYDRFRNRIMFPIHDPKGRVVGFGGRALGDE-KP 227
Query: 119 KYINSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTA 178
KY+NSPETPLF KS LYGL +A+ I K +++ EGYMDVI L Q G VA LGTA
Sbjct: 228 KYLNSPETPLFKKSELLYGLHKARKEIRKEKELILVEGYMDVIALHQAGIKNAVASLGTA 287
Query: 179 CTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDS 238
T HIK + Y + II FDGD+AGR+AA RA+E+ L +K + LP DPD
Sbjct: 288 LTEEHIKLLKRYADEIILCFDGDKAGRKAALRAIELLLPLG---INVKVIKLPGGKDPDE 344
Query: 239 YIRKFGYKIFSKKVLEAMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPLSSS 297
Y+RK G + K + + SL++F + ++ NYNL T EK+K +E L +I
Sbjct: 345 YLRKEGVEALKKLLENSKSLIEFLIARLLSNYNLDT--PEEKAKL-VEELLPLIKKIPD 400
>gnl|CDD|223435 COG0358, DnaG, DNA primase (bacterial type) [DNA replication,
recombination, and repair].
Length = 568
Score = 236 bits (604), Expect = 5e-72
Identities = 135/445 (30%), Positives = 213/445 (47%), Gaps = 23/445 (5%)
Query: 4 ASDFYKIQLK-NSKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLDYN-NINTLA 61
A+ FY+ L A+ +L+ RGL E+I F LGYAP ++L L
Sbjct: 115 AAIFYQSSLDPEGAAALKYLETRGLAAELIAHFRLGYAPPN-DSLLPFLAKKEYREEKLE 173
Query: 62 SSGLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYI 121
GL+ K + K YDRFR RIMFPI++ G +IGFGGR + ++ KY+
Sbjct: 174 DLGLLKRK------------EGKIYDRFRNRIMFPIRDLRGDVIGFGGR-VLGDDKPKYL 220
Query: 122 NSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACTS 181
NSPET LF K ELYGL A+ I K+ +++ EGYMDVI L + G VA LGTA T
Sbjct: 221 NSPETELFKKGEELYGLDPARKKIAKADQIIVVEGYMDVIALHKAGIKNAVASLGTALTE 280
Query: 182 THIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIR 241
HIK + +I FDGD+AGR+AA+RAL++ L + + LPD DPD IR
Sbjct: 281 EHIKLLSRGKKKVILCFDGDRAGRKAAKRALQLVLPLDFV--GVFVILLPDGKDPDELIR 338
Query: 242 KFGYKIFSKKVLEAMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPLSSSLRFK 301
K G + KK+ L FL E ++ NL T + + + I LR
Sbjct: 339 KEGAEALRKKLPNERLPLIEFLIEYLIPSNLDTEGKARLVEEAVPLIKVIP--DEVLRDY 396
Query: 302 IISSLSKIIKVSFNEINNLFKINTSSIKHKTIEKKNIQPICIEYQIMKLLISYPSLINEI 361
+ L++++ +S + + L ++ K+N I I + +++ I +
Sbjct: 397 YLQKLAELLGISDDALLQLQVQPEKK-ATQSPFKQNPGRIAIALLVQNPVLAPKQPILKA 455
Query: 362 NSEDMIIFSKCSQNYVKMFFQLIDTIHIFKNDIDHSKFIKYLKKINKNFE--SIIVKIQD 419
E ++ + + F + F +++ S F L+++ + + ++ K
Sbjct: 456 LLERPLLKLLLFEELLLELFGTPEIDARFLDELFQSLFEVLLEELVELLDINLLVSKAAI 515
Query: 420 NFEYSIEIAKKTLLDAIYKDRKSVV 444
F+ I + ++ L A+ K K+++
Sbjct: 516 VFDGVITLLQRLLDQALEKGLKNLI 540
>gnl|CDD|219773 pfam08275, Toprim_N, DNA primase catalytic core, N-terminal domain.
Length = 128
Score = 150 bits (381), Expect = 3e-44
Identities = 62/139 (44%), Positives = 80/139 (57%), Gaps = 14/139 (10%)
Query: 7 FYKIQLKNS--KEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLDYN-NINTLASS 63
FY LK + A ++LK RGL+ E I RF LGYAP+ W+ L ++ L +
Sbjct: 1 FYHELLKTKEGEAARDYLKSRGLSPETIKRFGLGYAPDGWDNLLNHLEKKGFDLELLLEA 60
Query: 64 GLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINS 123
GL+V + E YDRFR RIMFPI++ G+++GFGGR + D KY+NS
Sbjct: 61 GLLVKR-----------EDGGYYDRFRNRIMFPIRDESGRVVGFGGRALDDEEPPKYLNS 109
Query: 124 PETPLFHKSNELYGLFEAK 142
PETPLF K LYGL EAK
Sbjct: 110 PETPLFKKGKVLYGLDEAK 128
>gnl|CDD|173784 cd03364, TOPRIM_DnaG_primases, TOPRIM_DnaG_primases: The
topoisomerase-primase (TORPIM) nucleotidyl
transferase/hydrolase domain found in the active site
regions of proteins similar to Escherichia coli DnaG.
Primases synthesize RNA primers for the initiation of
DNA replication. DnaG type primases are often closely
associated with DNA helicases in primosome assemblies.
The TOPRIM domain has two conserved motifs, one of which
centers at a conserved glutamate and the other one at
two conserved aspartates (DxD). This glutamate and two
aspartates, cluster together to form a highly acid
surface patch. The conserved glutamate may act as a
general base in nucleotide polymerization by primases.
The DXD motif may co-ordinate Mg2+, a cofactor required
for full catalytic function. E. coli DnaG is a single
subunit enzyme.
Length = 79
Score = 94.9 bits (237), Expect = 4e-24
Identities = 34/80 (42%), Positives = 46/80 (57%), Gaps = 3/80 (3%)
Query: 151 VLITEGYMDVIGLSQFGFLQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAARR 210
V++ EGYMDVI L Q G VA LGTA T + + +I +FDGD+AG++AA R
Sbjct: 3 VILVEGYMDVIALHQAGIKNVVASLGTALTEEQAELLKRLAKEVILAFDGDEAGQKAALR 62
Query: 211 ALEVCLLYATDDKIIKFLFL 230
ALE+ L ++ L L
Sbjct: 63 ALELLL---KLGLNVRVLTL 79
>gnl|CDD|173779 cd01029, TOPRIM_primases, TOPRIM_primases: The
topoisomerase-primase (TORPIM) nucleotidyl
transferase/hydrolase domain found in the active site
regions of bacterial DnaG-type primases and their
homologs. Primases synthesize RNA primers for the
initiation of DNA replication. DnaG type primases are
often closely associated with DNA helicases in primosome
assemblies. The TOPRIM domain has two conserved motifs,
one of which centers at a conserved glutamate and the
other one at two conserved aspartates (DxD). This
glutamate and two aspartates, cluster together to form a
highly acid surface patch. The conserved glutamate may
act as a general base in nucleotide polymerization by
primases. The DXD motif may co-ordinate Mg2+, a cofactor
required for full catalytic function. The prototypical
bacterial primase. Escherichia coli DnaG is a single
subunit enzyme.
Length = 79
Score = 85.4 bits (212), Expect = 1e-20
Identities = 32/80 (40%), Positives = 47/80 (58%), Gaps = 3/80 (3%)
Query: 151 VLITEGYMDVIGLSQFGFLQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAARR 210
V+I EGYMDV+ L Q G VA LGTA T ++ + + ++I +FD D+AG++AA R
Sbjct: 3 VIIVEGYMDVLALHQAGIKNVVAALGTANTEEQLRLLKRFARTVILAFDNDEAGKKAAAR 62
Query: 211 ALEVCLLYATDDKIIKFLFL 230
ALE+ L ++ L
Sbjct: 63 ALELLLAL---GGRVRVPPL 79
>gnl|CDD|221942 pfam13155, Toprim_2, Toprim-like. This is a family or Toprim-like
proteins.
Length = 90
Score = 64.6 bits (158), Expect = 3e-13
Identities = 31/92 (33%), Positives = 46/92 (50%), Gaps = 7/92 (7%)
Query: 153 ITEGYMDVIGLSQFGFLQT----VAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAA 208
+ EG +D + L Q G VA LGTA T K + Y +I +FD D+AGR+AA
Sbjct: 2 VFEGAIDALSLYQLGQENNKAVVVATLGTALTEAQAKLLKRYAKEVILAFDNDKAGRKAA 61
Query: 209 RRALEVCLLYATDDKIIKFLFLPDKYDPDSYI 240
R + + + +K + LPD D + Y+
Sbjct: 62 ERLQK---ILKEEGLEVKVVLLPDGKDWNDYL 90
>gnl|CDD|222298 pfam13662, Toprim_4, Toprim domain. The toprim domain is found in
a wide variety of enzymes involved in nucleic acid
manipulation.
Length = 81
Score = 63.8 bits (156), Expect = 5e-13
Identities = 26/80 (32%), Positives = 38/80 (47%), Gaps = 3/80 (3%)
Query: 149 GYVLITEGYMDVIGLSQFGFLQTVAILGTACTSTH---IKKILFYTNSIIFSFDGDQAGR 205
+ I EGY DV+ L Q G+ VA+LG A + + + +I +FDGD AG
Sbjct: 1 STICIVEGYADVLALEQAGYKGVVAVLGGALSPLDGIGPEDLNIDVKEVILAFDGDVAGE 60
Query: 206 RAARRALEVCLLYATDDKII 225
+AA R E+ L +
Sbjct: 61 KAALRLAELLLALGVKVTRL 80
>gnl|CDD|214695 smart00493, TOPRIM, topoisomerases, DnaG-type primases, OLD family
nucleases and RecR proteins.
Length = 75
Score = 50.0 bits (120), Expect = 4e-08
Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 4/70 (5%)
Query: 151 VLITEGYMDVIGLSQFGFLQTVAI--LGTACTSTHIKKI--LFYTNSIIFSFDGDQAGRR 206
++I EG D I L + G + + G + IK + L +I + D D+ G
Sbjct: 3 LIIVEGPADAIALEKAGGKRGNVVALGGHLLSKEQIKLLKKLAKKAEVILATDPDREGEA 62
Query: 207 AARRALEVCL 216
A E+
Sbjct: 63 IAWELAELLK 72
>gnl|CDD|173773 cd00188, TOPRIM, Topoisomerase-primase domain. This is a
nucleotidyl transferase/hydrolase domain found in type
IA, type IIA and type IIB topoisomerases, bacterial
DnaG-type primases, small primase-like proteins from
bacteria and archaea, OLD family nucleases from
bacterial and archaea, and bacterial DNA repair proteins
of the RecR/M family. This domain has two conserved
motifs, one of which centers at a conserved glutamate
and the other one at two conserved aspartates (DxD).
This glutamate and two aspartates, cluster together to
form a highly acid surface patch. The conserved
glutamate may act as a general base in nucleotide
polymerization by primases and in strand joining in
topoisomerases and, as a general acid in strand cleavage
by topisomerases and nucleases. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 83
Score = 47.8 bits (114), Expect = 3e-07
Identities = 22/82 (26%), Positives = 36/82 (43%), Gaps = 4/82 (4%)
Query: 150 YVLITEGYMDVIGLSQFGF--LQTVAILGTACTST--HIKKILFYTNSIIFSFDGDQAGR 205
++I EG D + L+Q G VA+ G A T +K++L +I + D D+ G
Sbjct: 2 KLIIVEGPSDALALAQAGGYGGAVVALGGHALNKTRELLKRLLGEAKEVIIATDADREGE 61
Query: 206 RAARRALEVCLLYATDDKIIKF 227
A R LE+ + +
Sbjct: 62 AIALRLLELLKSLGKKVRRLLL 83
>gnl|CDD|216679 pfam01751, Toprim, Toprim domain. This is a conserved region from
DNA primase. This corresponds to the Toprim domain
common to DnaG primases, topoisomerases, OLD family
nucleases and RecR proteins. Both DnaG motifs IV and V
are present in the alignment, the DxD (V) motif may be
involved in Mg2+ binding and mutations to the conserved
glutamate (IV) completely abolish DnaG type primase
activity. DNA primase EC:2.7.7.6 is a
nucleotidyltransferase it synthesises the
oligoribonucleotide primers required for DNA replication
on the lagging strand of the replication fork; it can
also prime the leading stand and has been implicated in
cell division. This family also includes the atypical
archaeal A subunit from type II DNA topoisomerases. Type
II DNA topoisomerases catalyze the relaxation of DNA
supercoiling by causing transient double strand breaks.
Length = 86
Score = 47.3 bits (113), Expect = 4e-07
Identities = 23/74 (31%), Positives = 31/74 (41%), Gaps = 6/74 (8%)
Query: 151 VLITEGYMDVIGLSQFG---FLQTVAILGTACTSTHIK---KILFYTNSIIFSFDGDQAG 204
++I EG D I L + G VA G A HIK K L +I + D D+ G
Sbjct: 2 LIIVEGPSDAIALEKAGGVLGGAVVATSGHALDLEHIKELKKALKGAKEVILATDPDREG 61
Query: 205 RRAARRALEVCLLY 218
A + LE+
Sbjct: 62 EAIALKLLELLKPL 75
>gnl|CDD|222844 PHA02031, PHA02031, putative DnaG-like primase.
Length = 266
Score = 40.2 bits (94), Expect = 0.001
Identities = 35/163 (21%), Positives = 55/163 (33%), Gaps = 38/163 (23%)
Query: 86 YDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINSPETPLFHKSNELYG-----LFE 140
Y +GR++F G+ GR D K++ YG
Sbjct: 112 YSERQGRLIFRTDA------GWLGRATADQQ-PKWVG-------------YGYPAPDYVG 151
Query: 141 AKNAIEKSGYVLITEGYMDVIGLS---QFGFLQTVAILGTACTSTHIKKILFYT-NSIIF 196
+ V++TE Y+ + + + VA+LGT +L T ++
Sbjct: 152 WPPELSMPRPVVLTEDYLSALKVRWACNKPEVFAVALLGTRLRDRLAAILLQQTCPRVLI 211
Query: 197 SFDGDQAGR---RAARRALEVCLLYATDDKIIKFLFLPDKYDP 236
DGD AG A R L L + + PD +DP
Sbjct: 212 FLDGDPAGVDGSAGAMRRLRPLL------IEGQVIITPDGFDP 248
>gnl|CDD|236314 PRK08624, PRK08624, hypothetical protein; Provisional.
Length = 373
Score = 39.5 bits (92), Expect = 0.003
Identities = 32/110 (29%), Positives = 52/110 (47%), Gaps = 7/110 (6%)
Query: 86 YDRFRGRIMFPIKNTDGQIIGFGGRLIKDS--NEAKYINS--PETPLFH-KSNELYGLFE 140
D RI+ P ++ G++IG GRL+ ++ KY +T H K LYGL++
Sbjct: 177 LDVISQRIIIPHRDESGELIGIRGRLLDKELVDKNKYFPIYVNDTGYNHPKGKILYGLWQ 236
Query: 141 AKNAIEKSGYVLITEGYMDVIGLSQFGFLQ--TVAILGTACTSTHIKKIL 188
K I++ V+I E V+ +F VAI G+ + +K+L
Sbjct: 237 NKKYIKEKKKVIIVESEKSVLFSDKFYGEGNFVVAICGSNISEVQAEKLL 286
>gnl|CDD|222863 PHA02540, 61, DNA primase; Provisional.
Length = 337
Score = 38.0 bits (89), Expect = 0.006
Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 7/68 (10%)
Query: 92 RIMFPIKNTDGQIIGFGGRLIKDSNEAKYINSPETPLFHKSNELYGLFEAKNAIEKSGYV 151
R++ PI N DG+I F GR ++ KYI ++ ++YGL + I+ V
Sbjct: 173 RLVIPIFNKDGKIESFQGRALRKDAPQKYIT---IKADEEATKIYGL----DRIDPGKTV 225
Query: 152 LITEGYMD 159
+ EG +D
Sbjct: 226 YVVEGPID 233
>gnl|CDD|222074 pfam13362, Toprim_3, Toprim domain. The toprim domain is found in
a wide variety of enzymes involved in nucleic acid
manipulation.
Length = 95
Score = 35.3 bits (82), Expect = 0.007
Identities = 21/99 (21%), Positives = 36/99 (36%), Gaps = 10/99 (10%)
Query: 150 YVLITEGYMDVIGLSQFGF-LQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQA--GRR 206
++I EG + L + VA+LG +I + D D+A G++
Sbjct: 1 ILIIGEGIETALSLRRALPGAPVVAVLGANNLKAVAPP--ERGRRVIIAADNDKANAGQK 58
Query: 207 AARRALEVCLLYATDDKIIKFLFLPDKY-DPDSYIRKFG 244
AA + E I + P + D + +R G
Sbjct: 59 AAEKLAERL----EAAGIEVSVLEPPEGEDFNDDLRALG 93
>gnl|CDD|130673 TIGR01612, 235kDa-fam, reticulocyte binding/rhoptry protein. This
model represents a group of paralogous families in
plasmodium species alternately annotated as reticulocyte
binding protein, 235-kDa family protein and rhoptry
protein. Rhoptry protein is localized on the cell surface
and is extremely large (although apparently lacking in
repeat structure) and is important for the process of
invasion of the RBCs by the parasite. These proteins are
found in P. falciparum, P. vivax and P. yoelii.
Length = 2757
Score = 36.6 bits (84), Expect = 0.034
Identities = 46/159 (28%), Positives = 71/159 (44%), Gaps = 8/159 (5%)
Query: 275 IKDIEKSKYNIEYLFKIIPLSSSLRFKIISSLSKIIKVSFNEINNLFKINTSSIKHKTIE 334
IKDIEK + N ++ K S + II S K+ E+ F I+ K IE
Sbjct: 2080 IKDIEKFENNYKHSEKDNHDFSEEKDNIIQSKKKL-----KELTEAFNTEIKIIEDKIIE 2134
Query: 335 KKNIQPICIEYQIMKLLISYPSLINEINSE--DMIIFSKCSQNYVKMFFQLIDTIHIFKN 392
K ++ IE + LL SY +L+ + S+ + F + + K FF+ I+ I N
Sbjct: 2135 KNDLIDKLIEMRKECLLFSYATLVETLKSKVINHSEFITSAAKFSKDFFEFIEDISDSLN 2194
Query: 393 DIDHSKFIKY-LKKINKNFESIIVKIQDNFEYSIEIAKK 430
D + IKY L + K+ SI+ + IE K+
Sbjct: 2195 DDIDALQIKYNLNQTKKHMISILADATKDHNNLIEKEKE 2233
>gnl|CDD|129732 TIGR00646, MG010, DNA primase-related protein. The DNA primase
DnaG of E. coli and its apparent orthologs in other
eubacterial species are approximately 600 residues in
length. Within this set, a conspicuous outlier in
percent identity, as seen in a UPGMA difference tree, is
the branch containing the Mycoplasmas. This lineage is
also unique in containing the small, DNA primase-related
protein modelled by This model, which is homologous to
the central third of DNA primase. Several small regions
of sequence similarity specifically to Mycoplasma
sequences rather than to all DnaG homologs suggests that
the divergence of this protein from DnaG post-dated the
separation of bacterial lineages. The function of this
DNA primase-related protein is unknown [Unknown
function, General].
Length = 218
Score = 34.5 bits (79), Expect = 0.072
Identities = 32/119 (26%), Positives = 48/119 (40%), Gaps = 12/119 (10%)
Query: 95 FPIKNTDGQIIGFGGRLIKDSNEAKYINSPETPLFHKSNELYGLFEAKNAIEKSGYVLIT 154
P+ N DG +IGF R K E +++ P KS GL K + + +
Sbjct: 62 LPLYNFDGNLIGFLNR--KVGFEKEFLYLPFNKPPSKSEAFLGL---KELPIEDNSIYLV 116
Query: 155 EGYMDVIGLSQFGFLQTVAILGTACTSTHIKKILFYTNS----IIFSFDGDQAGRRAAR 209
EG D + + G L + + G + +K F+ I FD D AG+ AA
Sbjct: 117 EGDFDWLAFRKAGILNCLPLCGLTISDKQMK---FFKQKKIEKIFICFDNDFAGKNAAA 172
>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated.
Length = 1437
Score = 33.7 bits (78), Expect = 0.27
Identities = 28/149 (18%), Positives = 54/149 (36%), Gaps = 17/149 (11%)
Query: 286 EYLFKIIPLSSSLRFKIISSLSKIIKVSFNEINNLFKINTSSIKHKTIEKKNIQPICIEY 345
+ L I + L+ + + S +I KV ++ + ++ + ++ NI PI
Sbjct: 8 KKLLDQINIPDDLQSEALESA-EIEKVVVDKKSKKWEFH--------LKFPNILPIEDFK 58
Query: 346 QIMKLLISYPSLINEINSEDMIIFSK--CSQNYVKMFFQLIDTIHIFKNDIDHSKFIKYL 403
+ L S I +I I ++ + ++ I I K + F L
Sbjct: 59 LFKEKLKQSFSHIADIKVTFSIEVENITFTEELLLDYWNEI----IEKAKKNSPLFKSLL 114
Query: 404 KKINKNFE--SIIVKIQDNFEYSIEIAKK 430
KK E +I+K+ + E K
Sbjct: 115 KKQKVEVEGNKLIIKVNNEIERDHLKKKH 143
Score = 30.6 bits (70), Expect = 2.0
Identities = 28/199 (14%), Positives = 68/199 (34%), Gaps = 28/199 (14%)
Query: 258 LLQFFLEEIILNYNLKT-------IKDIEKSKYNIEYLFKIIPLSSSLRFKIISSLSKII 310
+ L++I + +L++ I+ + K + ++ F + + L + + +
Sbjct: 6 KFKKLLDQINIPDDLQSEALESAEIEKVVVDKKSKKWEFHLK-FPNILPIEDFKLFKEKL 64
Query: 311 KVSFNEINNL-----FKINTSSIKHKTIEKKNIQPICIEYQIMKLLISYPSLINEINSED 365
K SF+ I ++ ++ + + + +I++ L + +
Sbjct: 65 KQSFSHIADIKVTFSIEVENITFTEELLLD-------YWNEIIEKAKKNSPLFKSLLKKQ 117
Query: 366 MIIFSKCSQNYVKMFFQLIDTIHIFKNDIDHSKFIKYLKKINKNFESIIVKIQDNFEYSI 425
+ N + I + + D K + L K + F I+KI + S
Sbjct: 118 KVEVEG---NKLI-----IKVNNEIERDHLKKKHLPKLIKQYEKFGFGILKIDFEIDDSK 169
Query: 426 EIAKKTLLDAIYKDRKSVV 444
E +K +D K
Sbjct: 170 EELEKFEAQKEEEDEKLAK 188
>gnl|CDD|188527 TIGR04012, poly_gGlu_PgsB, poly-gamma-glutamate synthase PgsB/CapB.
Of four genes commonly found to be involved in
biosynthesis and export of poly-gamma-glutamate,
pgsB(capB) and pgsC(capC) are found to be involved in
the synthesis per se. Members of this family are
designated PgsB, a nomeclature that covers both cases in
which the poly-gamma-glutamate is secreted and those in
which it is retained to form capsular material.PgsB has
been shown to have poly-gamma-glutamate activity by
itself but is bound tightly by PgsC (TIGR04011) [Cell
envelope, Other].
Length = 366
Score = 31.1 bits (71), Expect = 1.0
Identities = 33/126 (26%), Positives = 51/126 (40%), Gaps = 28/126 (22%)
Query: 138 LFEAKNAIEKSGYVLIT---EGYMDVIGLSQFGFLQTVAILGTACTSTHIKKILFYTNSI 194
+FE K + K+ +IT E +MDV+G + L VA TA + LF
Sbjct: 105 VFELK--LVKANIGVITNVREDHMDVMGPT----LDDVAEAFTA--TIPYNGDLFTAEDD 156
Query: 195 IFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFGYKIFSKKVLE 254
F + A R + L D + I D +RKFGY +F + V
Sbjct: 157 YLDFFKEAAKDRNTK-------LIVADAEEI----------SDDILRKFGYIVFPENVAL 199
Query: 255 AMSLLQ 260
A+++ +
Sbjct: 200 ALAVAE 205
>gnl|CDD|225249 COG2374, COG2374, Predicted extracellular nuclease [General
function prediction only].
Length = 798
Score = 30.2 bits (68), Expect = 2.9
Identities = 10/55 (18%), Positives = 20/55 (36%), Gaps = 2/55 (3%)
Query: 56 NINTLASSGLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGR 110
++ T A + L V+ + + I +Y + + N Q + GG
Sbjct: 4 SLLTAALTLLSVEGVTVPQAATLAISEY--VEGSGNNKAIEVYNPYSQSVDLGGY 56
>gnl|CDD|205430 pfam13250, DUF4041, Domain of unknown function (DUF4041). This
presumed domain is functionally uncharacterized. This
domain family is found in bacteria, archaea and viruses,
and is approximately 60 amino acids in length. The
family is found in association with pfam10544.
Length = 56
Score = 26.3 bits (59), Expect = 6.1
Identities = 12/41 (29%), Positives = 23/41 (56%)
Query: 296 SSLRFKIISSLSKIIKVSFNEINNLFKINTSSIKHKTIEKK 336
+ +++ I ++ K I+ SF +IN L + N I + +E K
Sbjct: 16 AKVKYNNIDTMEKRIEKSFEQINKLGETNNIRISPEYLELK 56
>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 = 29.0 bits (65), Expect = 6.6
Identities = 27/131 (20%), Positives = 59/131 (45%), Gaps = 22/131 (16%)
Query: 309 IIKVSFNEINNLFKINTSSIKHKTIE--KKNIQPICIEYQIMKLLISYPSLI--NEINSE 364
+K+ F+ I+ F +N + I+ KK +Q + I+ +L + P+++ E+ E
Sbjct: 253 KVKILFSIISARFDVNAGLSGYMPIDQWKKCLQNM---LSILDILDANPNIVVVEEVADE 309
Query: 365 DMIIFSKCSQNYVKMFFQLIDTIHIFKNDIDHSKFIKYLKKIN-------------KNFE 411
++ ++Y ++ +I F +D +F K L+ I+ +F
Sbjct: 310 VEEDENETPEDYDGP-IRVQGSIVAFVERLD-DEFFKSLQNIDPHSNDYVERLKDEPSFY 367
Query: 412 SIIVKIQDNFE 422
++I ++QD E
Sbjct: 368 ALIERVQDYLE 378
>gnl|CDD|218749 pfam05788, Orbi_VP1, Orbivirus RNA-dependent RNA polymerase (VP1).
This family consists of the RNA-dependent RNA polymerase
protein VP1 from the Orbiviruses. VP1 may have both
enzymatic and structural roles in the virus life cycle.
Length = 1301
Score = 29.0 bits (65), Expect = 7.0
Identities = 9/47 (19%), Positives = 19/47 (40%)
Query: 313 SFNEINNLFKINTSSIKHKTIEKKNIQPICIEYQIMKLLISYPSLIN 359
S E N + ++ I + I P + ++ + + +P IN
Sbjct: 207 SILEFNAIMRMKEEGIHELEFGDEKIDPFDLVRELFIICLPHPKKIN 253
>gnl|CDD|182093 PRK09819, PRK09819, alpha-mannosidase; Provisional.
Length = 875
Score = 28.4 bits (64), Expect = 9.3
Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 12/77 (15%)
Query: 247 IFSKKVLEAMSLLQF-FLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPLSSSLRFKIISS 305
I S + + ++ + + ++ Y L K++E+ + + + K++ +
Sbjct: 543 ITSAEAVPSVEISHSAWQSRAVIRYRLAVPKNLEERAAGQK--------TGRMPVKLVVT 594
Query: 306 LSK---IIKVSFNEINN 319
LSK I N N
Sbjct: 595 LSKNSRRIDFDVNLDNQ 611
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.323 0.140 0.394
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,125,441
Number of extensions: 2384527
Number of successful extensions: 3064
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3014
Number of HSP's successfully gapped: 196
Length of query: 444
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 344
Effective length of database: 6,502,202
Effective search space: 2236757488
Effective search space used: 2236757488
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 61 (27.2 bits)