RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13396
(328 letters)
>gnl|CDD|240130 cd04860, AE_Prim_S, AE_Prim_S: primase domain similar to that found
in the small subunit of archaeal and eukaryotic (A/E)
DNA primases. Primases are DNA-dependent RNA polymerases
which synthesis the short RNA primers required for DNA
replication. In addition to its catalytic role in
replication, DNA primase may play a role in coupling
replication to DNA damage repair and in checkpoint
control during S phase. In eukaryotes, this small
catalytically active primase subunit (p50) and a larger
primase subunit (p60), referred to jointly as the core
primase, associate with the B subunit and the DNA
polymerase alpha subunit in a complex, called Pol
alpha-pri. The function of the larger primase subunit is
unclear. Included in this group are Pfu41 and Pfu46,
these two proteins comprise the primase complex of the
archaea Pyrococcus furiosus; Pfu41 and Pfu46 have
sequence identity to the eukaryotic p50 and p60 primase
proteins respectively. Pfu41 preferentially uses dNTPs
as substrate. Pfu46 regulates the primase activity of
Pfu41.
Length = 232
Score = 220 bits (562), Expect = 4e-71
Identities = 85/198 (42%), Positives = 109/198 (55%), Gaps = 12/198 (6%)
Query: 23 PYGPYLRWLFYG--NLDNFRKREFSFTLNGDIYARYISYNSPNELKKDLIKRCPQKIDLG 80
P +L YG D REF FTL +Y R++S++S EL+K L++ P+
Sbjct: 1 PSLFRYYYLNYGLEIPDYLENREFGFTLFDGVYIRHLSFSSAEELRKYLLRNVPR----- 55
Query: 81 AIYDICPKDHLQH--SVFTPKMKELVFDIDMTDYDDVRNCCSGADICEKCWRYMSIACKI 138
A+Y +ELVFDID DYDDVR CCSGA ICEKCW++ A KI
Sbjct: 56 AVYSSSAYYRKPSAKGEKGWLGRELVFDIDADDYDDVRTCCSGATICEKCWKFAKEAVKI 115
Query: 139 LDTALREDFDFQLLLWVFSGRRGIHCWVCDEAALALDGRGRSCLAEYMSVLTANPVKKV- 197
LD LREDF F+ +LWVFSGRRG H WVCDE A LD R + +Y++ + N K
Sbjct: 116 LDDILREDFGFKHILWVFSGRRGYHVWVCDEKARKLDSDERREIVDYLNGIGLNEDKIKK 175
Query: 198 --FLTGDVLHPHLKRAKL 213
G LHP ++RA +
Sbjct: 176 VKVNLGRPLHPGIRRALI 193
Score = 61.1 bits (149), Expect = 6e-11
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 301 RLDIHVSKGVNHLLKSPFCVHPKTGKIC 328
+D +V+K +N LL+ PF +H KTG I
Sbjct: 192 LIDENVTKDINRLLRLPFSLHGKTGLIV 219
>gnl|CDD|224384 COG1467, PRI1, Eukaryotic-type DNA primase, catalytic (small)
subunit [DNA replication, recombination, and repair].
Length = 341
Score = 163 bits (414), Expect = 1e-47
Identities = 82/304 (26%), Positives = 125/304 (41%), Gaps = 35/304 (11%)
Query: 36 LDNFRKREFSFTLNGDIYARYISYNSPNELKKDLIKRCPQKIDLGAIYDICPKDHLQHSV 95
LD + EF F L G +Y R++S+ S EL+ L + P+ + A Y PK+
Sbjct: 30 LDIDEREEFYFPLKGGVYDRHLSFRSERELRDYLRRNAPRHVYSSAAYYEKPKER----- 84
Query: 96 FTPKM-------KELVFDIDMTDYDDVRNCCSGADICEKCWRYMSIACKILDTALREDFD 148
KM ELVFDID + R C +C+ C A ++L+ LREDF
Sbjct: 85 ---KMEEKGWLGAELVFDIDADHLPERR--CDKDSVCKMCLEDKKEAVRLLNDFLREDFG 139
Query: 149 FQLLLWVFSGRRGIHCWVCDEAALALDGRGRSCLAEYMSVLTANPVKKVFLTGDVLHPHL 208
F+ + VFSGRRG H V DE L+L R + +Y+S + L L
Sbjct: 140 FKDIKIVFSGRRGYHVHVSDEEVLSLGSEERREILDYVSGNRLEL--ETVFRLRPLKRLL 197
Query: 209 KRAKLIIEDQFEKLLEEQELLSTKERQTKVLGLVSNGDIRAEIEK-EWTRIGPGQDVEKW 267
R + F KL + L + DI + + R+ D +
Sbjct: 198 GRVLGWGKGLFIKLRLREARLMKRV----------KEDIENALARLPDKRLI-AIDEKVT 246
Query: 268 D---RLVAIIKHHQAKNSDRKLKYAIEEILLELAYPRLDIHVSKGVNHLLKSPFCVHPKT 324
+ RL+ + K + ++E L + LD V+K + LL+ P +H K
Sbjct: 247 NDITRLIRLPGSLDGKGFLTVARLGLDE-LRVFSPLYLDGEVTKDLKRLLRLPGSLHSKL 305
Query: 325 GKIC 328
G++
Sbjct: 306 GEVK 309
>gnl|CDD|216771 pfam01896, DNA_primase_S, Eukaryotic and archaeal DNA primase small
subunit. DNA primase synthesises the RNA primers for
the Okazaki fragments in lagging strand DNA synthesis.
DNA primase is a heterodimer of large and small
subunits. This family also includes baculovirus late
expression factor 1 or LEF-1 proteins. Baculovirus LEF-1
is a DNA primase enzyme. Bacterial DNA primase adopts a
different fold to archaeal and eukaryotic primases.
Length = 133
Score = 91.1 bits (226), Expect = 1e-22
Identities = 39/81 (48%), Positives = 51/81 (62%), Gaps = 2/81 (2%)
Query: 105 FDIDMTDYDDVRNCCSGADICEKCWRYMSIACKILDTALREDFDFQLLLWVFSGRRGIHC 164
FDID DYDDVR CCS A++ KC +++ A ++LD AL EDF L VFSG+RG H
Sbjct: 1 FDIDFDDYDDVRTCCSIANV--KCIKFVVNAARVLDRALLEDFGVTHTLVVFSGKRGFHL 58
Query: 165 WVCDEAALALDGRGRSCLAEY 185
WV + A +L R +A+Y
Sbjct: 59 WVPFKEARSLGDARRREIADY 79
Score = 44.5 bits (105), Expect = 9e-06
Identities = 21/51 (41%), Positives = 28/51 (54%), Gaps = 7/51 (13%)
Query: 285 KLKYAIEEILLE-------LAYPRLDIHVSKGVNHLLKSPFCVHPKTGKIC 328
A E LLE PRLD+ V+KG+ HL++ PF HPKTG++
Sbjct: 78 DYAKAFAETLLEEQDDFPTATKPRLDVLVTKGIRHLIRLPFSRHPKTGRVS 128
>gnl|CDD|232925 TIGR00335, primase_sml, DNA primase, eukaryotic-type, small
subunit, putative. Archaeal members differ
substantially from eukaryotic members and should be
considered putative pending experimental evidence. The
protein is universal and single copy among completed
archaeal and eukarotic genomes to date. DNA primase
creates RNA primers needed for DNA replication.This
model is named putative because the assignment is
putative for archaeal proteins. Eukaryotic proteins
scoring above the trusted cutoff can be considered
authentic [DNA metabolism, DNA replication,
recombination, and repair].
Length = 297
Score = 94.6 bits (235), Expect = 3e-22
Identities = 72/317 (22%), Positives = 108/317 (34%), Gaps = 54/317 (17%)
Query: 17 YYKRIFPYGPYLRWLFY--GNLDNFRKREFSFTLNGDIY-ARYISYNSPNELKKDLIKRC 73
YYK + + L F REF + ++ RY S+ LK K
Sbjct: 6 YYKEKYNFYYSKNELELPRKFNREFAFREFGLLPDFVMHRHRYESFFRERILKNVPAKIY 65
Query: 74 PQKIDLGAIYDICP--KDHLQHSVFTPKMKELVFDIDMTDYDDVRNCCSGADICEKCWRY 131
P Y+ P + L + EL FDID+ D + C G
Sbjct: 66 PSSAYYSRAYEDKPEKRGWLGKGLI---RDELAFDIDVKDQSFEKAECDG--KQVCLEEA 120
Query: 132 MSIACKILDTALREDFDFQLLLWVFSGRRGIHCWVCDEAALALDGRGRSCLAEYMSVLTA 191
+A DT LR DF VFSG RG H V D + L E +
Sbjct: 121 KLLAVLRADTGLR-DFGLYDSGGVFSGVRGYHEEVLDLGSRE--------LREIVRYERL 171
Query: 192 NPVKKVFLTGDVLHPHLKRAKLIIEDQFEKLLEEQELLSTKERQTKVLGLVSNGDIRAEI 251
K V + L+ + K ++ + E+E+L++K +
Sbjct: 172 RYPKIVRVEKRFLNSN--AVKRVLN-RLLLKALEEEILTSKLKILP-------------- 214
Query: 252 EKEWTRIGPGQDVEKWDRLVAIIKHHQAKNSDRKLKYAIEEILLELAYPRLDIHVSKGVN 311
D+ KW + +I S++K A+E + + LD V+
Sbjct: 215 ----------NDLRKWKLIKEVI-----FKSEKKDYSALEIYIDK---IVLDDKVTLDRI 256
Query: 312 HLLKSPFCVHPKTGKIC 328
LL+ P +H TG IC
Sbjct: 257 RLLRHPKSLHRVTGVIC 273
>gnl|CDD|238291 cd00525, AE_Prim_S_like, AE_Prim_S_like: primase domain similar to
that found in the small subunit of archaeal and
eukaryotic (A/E) DNA primases. The replication
machineries of A/Es are distinct from that of bacteria.
Primases are DNA-dependent RNA polymerases which
synthesis the short RNA primers required for DNA
replication. In eukaryotes, this small catalytically
active primase subunit (p50) and a larger primase
subunit (p60), referred to jointly as the core primase,
associate with the B subunit and the DNA polymerase
alpha subunit in a complex, called Pol alpha-pri. In
addition to its catalytic role in replication,
eukaryotic DNA primase may play a role in coupling
replication to DNA damage repair and in checkpoint
control during S phase. Pfu41 and Pfu46 comprise the
primase complex of the archaea Pyrococcus furiosus;
these proteins have sequence identity to the eukaryotic
p50 and p60 primase proteins respectively. Pfu41
preferentially uses dNTPs as substrate. Pfu46 regulates
the primase activity of Pfu41. Also found in this group
is the primase-polymerase (primpol) domain of replicases
from archaeal plasmids including the ORF904 protein of
pRN1 from Sulfolobus islandicus (pRN1 primpol). The pRN1
primpol domain exhibits DNA polymerase and primase
activities; a cluster of active site residues (three
acidic residues, and a histidine) is required for both
these activities. The pRN1 primpol primase activity
prefers dNTPs to rNTPs; however incorporation of dNTPs
requires rNTP as cofactor. This group also includes the
Pol domain of bacterial LigD proteins such Mycobacterium
tuberculosis (Mt)LigD. MtLigD contains an N-terminal Pol
domain, a central phosphoesterase module, and a
C-terminal ligase domain. LigD Pol plays a role in
non-homologous end joining (NHEJ)-mediated repair of DNA
double-strand breaks (DSB) in vivo, perhaps by filling
in short 5'-overhangs with ribonucleotides; the filled
in termini would be sealed by the associated LigD ligase
domain. The MtLigD Pol domain is stimulated by
manganese, is error-prone, and prefers adding rNTPs to
dNTPs in vitro.
Length = 136
Score = 66.6 bits (163), Expect = 1e-13
Identities = 32/132 (24%), Positives = 42/132 (31%), Gaps = 31/132 (23%)
Query: 42 REFSFTLNG--DIYARYISY---NSPNELKKDLIKRCPQKIDLGAIYDICPKDHLQHSVF 96
R S + R+ + E+ L P G I +
Sbjct: 1 RPVSPIRPPGKGPFQRHWPFGATTDDAEILAWLANLPP-----GNIGLSLGRYDK----- 50
Query: 97 TPKMKELVFDIDMTDYDDVRNCCSGADICEKCWRYMSIACKILDTALREDFDFQLLLWVF 156
K LVFD+D DYD CW + A +L L ED L V
Sbjct: 51 LWKPDLLVFDLDPDDYD--------------CWEDVKEAALLLRELLDEDGL--NTLVVT 94
Query: 157 SGRRGIHCWVCD 168
SG RG+H +V
Sbjct: 95 SGSRGLHVYVRL 106
Score = 30.4 bits (69), Expect = 0.59
Identities = 10/27 (37%), Positives = 14/27 (51%), Gaps = 1/27 (3%)
Query: 299 YPRLDIHVSKGVNHLLKSPFCVHPKTG 325
+DI V+ LL +P VHP+ G
Sbjct: 104 VRLIDIRVNA-RGRLLVAPPSVHPRPG 129
>gnl|CDD|234755 PRK00419, PRK00419, DNA primase small subunit; Reviewed.
Length = 376
Score = 64.6 bits (158), Expect = 1e-11
Identities = 49/165 (29%), Positives = 71/165 (43%), Gaps = 36/165 (21%)
Query: 41 KREFSFTLNG----DIYARYISYNSPNELKKDLIKRCPQKIDLGAIYDICPKDHLQHSV- 95
KREF F G D R++S++ EL+ L + P+ H+ +SV
Sbjct: 30 KREFGFIPFGEGPSDTMVRHLSFSDLGELRDYLRRTAPR--------------HVYYSVA 75
Query: 96 -------FTPKMK-----ELVFDIDMTDYDDVRNCCSGADIC-EKCWRYMSIACKILDTA 142
T + K +L+FD+D VR C E+ A ++LD
Sbjct: 76 RYELPSARTMEEKGWLGADLIFDLDADHLPGVRCEEDSYCECLERAKE---EALRLLDF- 131
Query: 143 LREDFDFQLLLWVFSGRRGIHCWVCDEAALALDGRGRSCLAEYMS 187
L +DF F+ + VFSG RG H V DE L LD R + +Y+S
Sbjct: 132 LEDDFGFEDIHVVFSGGRGYHVHVRDEDVLELDSDERREIVDYVS 176
>gnl|CDD|182440 PRK10415, PRK10415, tRNA-dihydrouridine synthase B; Provisional.
Length = 321
Score = 32.6 bits (74), Expect = 0.22
Identities = 21/56 (37%), Positives = 26/56 (46%), Gaps = 12/56 (21%)
Query: 167 CDEAALALDGRGRSCL----AEYMSVLTANPVKK-----VFLTGDVLHPHLKRAKL 213
C AL + GR R+CL AEY S+ VK+ V GD+ P RA L
Sbjct: 161 CGIQALTIHGRTRACLFNGEAEYDSIRA---VKQKVSIPVIANGDITDPLKARAVL 213
>gnl|CDD|183219 PRK11593, folB, bifunctional dihydroneopterin
aldolase/dihydroneopterin triphosphate 2'-epimerase;
Provisional.
Length = 119
Score = 29.4 bits (66), Expect = 0.93
Identities = 15/33 (45%), Positives = 19/33 (57%), Gaps = 7/33 (21%)
Query: 101 KELVFDIDM-------TDYDDVRNCCSGADICE 126
++LVFDI+M DDV +C S ADI E
Sbjct: 26 QKLVFDIEMAWDNRKAAKSDDVADCLSYADIAE 58
>gnl|CDD|233067 TIGR00641, acid_CoA_mut_N, methylmalonyl-CoA mutase N-terminal
domain. Methylmalonyl-CoA mutase (EC 5.4.99.2)
catalyzes a reversible isomerization between
L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an
adenosylcobalamin cofactor. It may be a homodimer, as in
mitochondrion, or a heterodimer with partially
homologous beta chain that does not bind the
adenosylcobalamin cofactor, as in Propionibacterium
freudenreichii. The most similar archaeal sequences are
separate chains, such as AF2215 abd AF2219 of
Archaeoglobus fulgidus, that correspond roughly to the
first 500 and last 130 residues, respectively of known
methylmalonyl-CoA mutases. This model describes the
N-terminal domain subfamily. In a neighbor-joining tree,
AF2215 branches with a bacterial isobutyryl-CoA mutase,
which is also the same length. Scoring between the noise
and trusted cutoffs are the non-catalytic, partially
homologous beta chains from certain heterodimeric
examples of 5.4.99.2.
Length = 524
Score = 30.1 bits (68), Expect = 1.6
Identities = 14/60 (23%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 232 KERQTKVLGLVSNGDIRAEIEKEWTRIGPGQDVEKWDRLVAIIKHHQAKNSDRKLKYAIE 291
+E + +VL V N +R E + ++ +D EK + + + K + L AI+
Sbjct: 438 EEDEVEVLK-VDNSSVREEQIAKLKKLRAERDQEKVEAALDALTKAAEKEDENLLALAID 496
>gnl|CDD|236162 PRK08138, PRK08138, enoyl-CoA hydratase; Provisional.
Length = 261
Score = 29.6 bits (67), Expect = 1.9
Identities = 13/35 (37%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 169 EAALALDGRGRSCLAEYMSVLTANP-VKKVFLTGD 202
EA AL+ R LAE+ + L+ +P ++ + LTG
Sbjct: 27 EARNALNMEVRQQLAEHFTELSEDPDIRAIVLTGG 61
>gnl|CDD|215621 PLN03188, PLN03188, kinesin-12 family protein; Provisional.
Length = 1320
Score = 29.9 bits (67), Expect = 2.4
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 267 WDRLVAIIKHHQAKNSDRKLKYAIEEILLEL 297
++RL A I Q K++DR+LKY LE+
Sbjct: 207 FERLFARINEEQIKHADRQLKYQCRCSFLEI 237
>gnl|CDD|187552 cd05241, 3b-HSD-like_SDR_e, 3beta-hydroxysteroid dehydrogenases
(3b-HSD)-like, extended (e) SDRs. Extended SDR family
domains belonging to this subgroup have the
characteristic active site tetrad and a fairly
well-conserved NAD(P)-binding motif. 3b-HSD catalyzes
the NAD-dependent conversion of various steroids, such
as pregnenolone to progesterone, or androstenediol to
testosterone. This subgroup includes an unusual
bifunctional 3b-HSD/C-4 decarboxylase from Arabidopsis
thaliana, and Saccharomyces cerevisiae ERG26, a
3b-HSD/C-4 decarboxylase, involved in the synthesis of
ergosterol, the major sterol of yeast. It also includes
human 3 beta-HSD/HSD3B1 and C(27) 3beta-HSD/
[3beta-hydroxy-delta(5)-C(27)-steroid oxidoreductase;
HSD3B7]. C(27) 3beta-HSD/HSD3B7 is a membrane-bound
enzyme of the endoplasmic reticulum, that catalyzes the
isomerization and oxidation of 7alpha-hydroxylated
sterol intermediates, an early step in bile acid
biosynthesis. Mutations in the human NSDHL (NAD(P)H
steroid dehydrogenase-like protein) cause CHILD syndrome
(congenital hemidysplasia with ichthyosiform nevus and
limb defects), an X-linked dominant, male-lethal trait.
Mutations in the human gene encoding C(27) 3beta-HSD
underlie a rare autosomal recessive form of neonatal
cholestasis. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
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 numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, 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. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid sythase 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.
Length = 331
Score = 28.9 bits (65), Expect = 3.2
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 82 IYDICPKDHLQHSVFTPKMKELVFDIDMTDYDDVRNCCSGAD 123
+DI P + P ++ L DI TD +DV SGAD
Sbjct: 29 SFDIAPPGEALSAWQHPNIEFLKGDI--TDRNDVEQALSGAD 68
>gnl|CDD|226594 COG4109, COG4109, Predicted transcriptional regulator containing
CBS domains [Transcription].
Length = 432
Score = 28.9 bits (65), Expect = 3.8
Identities = 17/73 (23%), Positives = 31/73 (42%), Gaps = 10/73 (13%)
Query: 195 KKVFLTGDVLHPHLKRAKLIIEDQFEKLLE-EQELLSTK----ERQTKVLGLVSNGDI-- 247
K + D++ P + L D E L+ ++ ++ R KV+G+V+ D+
Sbjct: 185 KDIITVEDIMTPLEDTSYLRETDTVEDWLDLVEKTGHSRFPVVNRSMKVVGVVTMRDVLD 244
Query: 248 ---RAEIEKEWTR 257
IEK T+
Sbjct: 245 KKPSTTIEKVMTK 257
>gnl|CDD|139107 PRK12624, flgB, flagellar basal body rod protein FlgB; Provisional.
Length = 143
Score = 28.1 bits (62), Expect = 4.4
Identities = 10/33 (30%), Positives = 21/33 (63%)
Query: 206 PHLKRAKLIIEDQFEKLLEEQELLSTKERQTKV 238
PH KR+++I E ++ +E +++ KE T++
Sbjct: 38 PHFKRSEVIFESMIKRAIESEKIEKEKEVPTQI 70
>gnl|CDD|226531 COG4044, COG4044, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 247
Score = 27.9 bits (62), Expect = 6.1
Identities = 24/73 (32%), Positives = 34/73 (46%), Gaps = 10/73 (13%)
Query: 206 PHLKRAKLIIEDQFEKLLEEQELLSTKERQTKVLG--------LVSNGDIRAEIEKEWTR 257
HL + E KL +E E T ++ K+ G L+ NG R EIE+ R
Sbjct: 134 DHLPVEVEVNEV--NKLAQEIEARLTDKQVDKLKGWTSDSYDRLIINGATREEIERALNR 191
Query: 258 IGPGQDVEKWDRL 270
G G+DV + +RL
Sbjct: 192 TGHGRDVVRIERL 204
>gnl|CDD|129918 TIGR00838, argH, argininosuccinate lyase. This model describes
argininosuccinate lyase, but may include examples of
avian delta crystallins, in which argininosuccinate
lyase activity may or may not be present and the
biological role is to provide the optically clear
cellular protein of the eye lens [Amino acid
biosynthesis, Glutamate family].
Length = 455
Score = 28.1 bits (63), Expect = 7.0
Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 199 LTGDVLHPH-LKRAKLIIEDQFEKLLEEQELLSTKERQTKVLGLVSNGDIRAEIEKEWT- 256
+ G + H LK+A ++ E++ K++E L + R+ + + DI IE+E
Sbjct: 32 IEGSIAHTKMLKKAGILTEEEAAKIIEGLNELKEEGREGPFILDPDDEDIHMAIERELID 91
Query: 257 RIGPG 261
R+G
Sbjct: 92 RVGED 96
>gnl|CDD|200381 TIGR04130, FnlA, UDP-N-acetylglucosamine
4,6-dehydratase/5-epimerase. The FnlA enzyme is the
first step in the biosynthesis of UDP-FucNAc from
UDP-GlcNAc in E. coli (along with FnlB and FnlC). The
proteins identified by this model include FnlA homologs
in the O-antigen clusters of O4, O25, O26, O29 (Shigella
D11), O118, O145 and O172 serotype strains, all of which
produce O-antigens containing FucNAc (or the further
modified FucNAm). A homolog from Pseudomonas aerugiosa
serotype O11, WbjB, also involved in the biosynthesis of
UDP-FucNAc has been characterized and is now believed to
carry out both the initial 4,6-dehydratase reaction and
the subsequent epimerization of the resulting methyl
group at C-5. A phylogenetic tree of related sequences
shows a distinct clade of enzymes involved in the
biosynthesis of UDP-QuiNAc (Qui=qinovosamine). This
clade appears to be descendant from the common ancestor
of the Pseudomonas and E. coli fucose-biosynthesis
enzymes. It has been hypothesized that the first step in
the biosynthesis of these two compounds may be the same,
and thus that these enzymes all have the same function.
At present, lacking sufficient confirmation of this, the
current model trusted cutoff only covers the tree
segment surrounding the E. coli genes. The clades
containing the Pseudomonas and QuiNAc biosynthesis
enzymes score above the noise cutoff. Immediately below
the noise cutoff are enzymes involved in the
biosynthesis of UDP-RhaNAc (Rha=rhamnose), which again
may or may not produce the same product.
Length = 337
Score = 28.0 bits (62), Expect = 7.1
Identities = 23/94 (24%), Positives = 47/94 (50%), Gaps = 18/94 (19%)
Query: 226 QELLSTKERQTKVLG----------LVSNGDIRAEIEK-EWTRIGP-------GQDVEKW 267
+ELL+ E ++G L+S ++ A I+ ++ R+ P G+ VE
Sbjct: 239 KELLNAHEHPVNIIGTRHGEKLYEALLSREEMIAAIDMGDYYRVPPDLRDLNYGKYVEHG 298
Query: 268 DRLVAIIKHHQAKNSDRKLKYAIEEILLELAYPR 301
DR ++ ++ + + N+ R ++E+LL+L + R
Sbjct: 299 DRRISEVEDYNSHNTQRLDVEGMKELLLKLPFIR 332
>gnl|CDD|223409 COG0332, FabH, 3-oxoacyl-[acyl-carrier-protein].
Length = 323
Score = 28.0 bits (63), Expect = 7.3
Identities = 21/77 (27%), Positives = 28/77 (36%), Gaps = 14/77 (18%)
Query: 107 IDMTDYDDVRNCC------SGADICEKCWRYMSIACKILDTALREDFDFQLLLWVFSGRR 160
+D TD R+ C +GA + E ILDT L D LL++ G
Sbjct: 147 LDWTD----RDTCVLFGDGAGAVVLEAT----EDDNGILDTDLGSDGSQGDLLYLPGGGS 198
Query: 161 GIHCWVCDEAALALDGR 177
L +DGR
Sbjct: 199 ATPKEESGGGLLVMDGR 215
>gnl|CDD|226865 COG4458, SrfC, Uncharacterized protein conserved in bacteria,
putative virulence factor [Function unknown].
Length = 821
Score = 27.9 bits (62), Expect = 8.3
Identities = 13/32 (40%), Positives = 16/32 (50%)
Query: 170 AALALDGRGRSCLAEYMSVLTANPVKKVFLTG 201
LALD G S LAEY+S + +K L
Sbjct: 483 TLLALDDGGVSRLAEYLSAICLPEIKYGRLQE 514
>gnl|CDD|183981 PRK13333, PRK13333, pantothenate kinase; Reviewed.
Length = 206
Score = 27.2 bits (61), Expect = 9.0
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 2/30 (6%)
Query: 56 YISYNSPNELKKDLIKRCPQKIDLGAIYDI 85
YIS N EL+K L+K P I+L +++
Sbjct: 38 YISVN--EELEKKLLKCYPNAINLEPYFEL 65
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
0.324 0.141 0.446
Gapped
Lambda K H
0.267 0.0772 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,524,097
Number of extensions: 1740952
Number of successful extensions: 1622
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1607
Number of HSP's successfully gapped: 39
Length of query: 328
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 231
Effective length of database: 6,635,264
Effective search space: 1532745984
Effective search space used: 1532745984
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 59 (26.4 bits)