RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4725
(457 letters)
>gnl|CDD|211589 TIGR00588, ogg, 8-oxoguanine DNA-glycosylase (ogg). All proteins
in this family for which functions are known are
8-oxo-guanaine DNA glycosylases that function in base
excision repair. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University). This family is distantly realted
to the Nth-MutY superfamily [DNA metabolism, DNA
replication, recombination, and repair].
Length = 310
Score = 188 bits (478), Expect = 4e-56
Identities = 109/324 (33%), Positives = 157/324 (48%), Gaps = 48/324 (14%)
Query: 9 HLSGKILCPAIELSLTLTLLGGQSFRWKQLTSDEKKLGNRFQGVFK---ECVWTLWADPS 65
H I P EL L L L GQSFRW+ +E + G+ + VWTL
Sbjct: 3 HRWASIPIPRSELRLDLVLRSGQSFRWRW---EESP--AHWSGLLVIADQPVWTLTQTEE 57
Query: 66 YLHYQVFSQHKLNANSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVGIRMLNQ 125
L V+ K + +ET L++YF+LD +L +LY W + D F+ F G+R+L Q
Sbjct: 58 QLLCTVYRGDKPTQDELETKLEKYFQLDVSLAQLYTHWGSVDKHFQYVAQKFQGVRLLRQ 117
Query: 126 DLTENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSHAKSCPA 185
D E + SF+CSSNNNIARI+ M++++C+ +G + TLD
Sbjct: 118 DPFECLISFICSSNNNIARITRMVERLCQAFGPRLITLDG-------------------- 157
Query: 186 VTKFFAFPSIDALARPAVEAKLRQLGFGYRAKFIQKSAEYIIQG-GGESWLERLGGKSYE 244
VT + FPS+ AL P EA LR+LG GYRA++I+++A +++ GG +WL+++ G SYE
Sbjct: 158 VT-YHGFPSLHALTGPEAEAHLRKLGLGYRARYIRETARALLEEQGGRAWLQQIRGASYE 216
Query: 245 EAREELQRLPGIGAKVGD----------GVFKEHVWTLWADPSYLHYQVYSQHKLNT--- 291
+ARE L LPG+G KV D V + + Y H +
Sbjct: 217 DAREALCELPGVGPKVADCICLMGLDKPQAVPVDVHV-----WRIANRDYPWHPKTSRAK 271
Query: 292 NSVETMLKEYFRLDENLPELYAEW 315
KE +L YA W
Sbjct: 272 GPSPFARKELGNFFRSLWGPYAGW 295
Score = 72.6 bits (178), Expect = 4e-14
Identities = 38/78 (48%), Positives = 49/78 (62%), Gaps = 2/78 (2%)
Query: 327 GDFVADCICLMSLSHLQAVPVDTHVYQIACNHY--HFQKSTSKTLTPAVYNQIRAFFADK 384
G VADCICLM L QAVPVD HV++IA Y H + S +K +P ++ FF
Sbjct: 229 GPKVADCICLMGLDKPQAVPVDVHVWRIANRDYPWHPKTSRAKGPSPFARKELGNFFRSL 288
Query: 385 FGKYAGWAHSILFCADLK 402
+G YAGWA ++LF ADL+
Sbjct: 289 WGPYAGWAQAVLFSADLR 306
Score = 38.0 bits (88), Expect = 0.008
Identities = 22/61 (36%), Positives = 31/61 (50%)
Query: 269 VWTLWADPSYLHYQVYSQHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGD 328
VWTL L VY K + +ET L++YF+LD +L +LY W + D F+
Sbjct: 49 VWTLTQTEEQLLCTVYRGDKPTQDELETKLEKYFQLDVSLAQLYTHWGSVDKHFQYVAQK 108
Query: 329 F 329
F
Sbjct: 109 F 109
>gnl|CDD|219650 pfam07934, OGG_N, 8-oxoguanine DNA glycosylase, N-terminal domain.
The presence of 8-oxoguanine residues in DNA can give
rise to G-C to T-A transversion mutations. This enzyme
is found in archaeal, bacterial and eukaryotic species,
and is specifically responsible for the process which
leads to the removal of 8-oxoguanine residues. It has
DNA glycosylase activity (EC:3.2.2.23) and DNA lyase
activity (EC:4.2.99.18). The region featured in this
family is the N-terminal domain, which is organised into
a single copy of a TBP-like fold. The domain contributes
residues to the 8-oxoguanine binding pocket.
Length = 113
Score = 106 bits (266), Expect = 8e-28
Identities = 43/119 (36%), Positives = 58/119 (48%), Gaps = 6/119 (5%)
Query: 13 KILCPAIELSLTLTLLGGQSFRWKQLTSDEKKLGNRFQGVFKECVWTLWADPSYLHYQVF 72
+ EL L LTLL GQSFRWK K + GV V L D L Y+
Sbjct: 1 SLPLSKEELDLKLTLLSGQSFRWK------KTEDTSYTGVIGGRVVELKQDEDDLEYRFL 54
Query: 73 SQHKLNANSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVGIRMLNQDLTENI 131
+ L E L++YF LD +L +LY +WS +D F++ F G+R+L QD E +
Sbjct: 55 GKEDLKGKDAEEFLRDYFDLDVDLNDLYEQWSKKDPLFKKAADKFRGLRILRQDPFECL 113
Score = 58.8 bits (143), Expect = 8e-11
Identities = 22/67 (32%), Positives = 32/67 (47%)
Query: 263 GVFKEHVWTLWADPSYLHYQVYSQHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFF 322
GV V L D L Y+ + L E L++YF LD +L +LY +WS +D F
Sbjct: 33 GVIGGRVVELKQDEDDLEYRFLGKEDLKGKDAEEFLRDYFDLDVDLNDLYEQWSKKDPLF 92
Query: 323 RQTCGDF 329
++ F
Sbjct: 93 KKAADKF 99
>gnl|CDD|223200 COG0122, AlkA, 3-methyladenine DNA glycosylase/8-oxoguanine DNA
glycosylase [DNA replication, recombination, and
repair].
Length = 285
Score = 84.8 bits (210), Expect = 2e-18
Identities = 41/181 (22%), Positives = 62/181 (34%), Gaps = 33/181 (18%)
Query: 82 VETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVGIRMLNQDLTENIFSFLCSSNNN 141
+E L+ F LD +L + R L D E + + S +
Sbjct: 65 IEAALRRLFDLDPDLAPIIDALG-PLPLLRA----PGLRLPLAPDPFEALVRAILSQQVS 119
Query: 142 IARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSHAKSCPAVTKFFAFPSIDALARP 201
+A + + ++ YG A+ + +FP+ + LA
Sbjct: 120 VAAAAKIWARLVSLYGN--------------------------ALEIYHSFPTPEQLAAA 153
Query: 202 AVEAKLRQLGFGYRAKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAKVG 261
EA R G +A++I A GE L L S EEA EEL L GIG
Sbjct: 154 DEEALRRCGLSGRKAEYIISLARAAA--EGELDLSELKPLSDEEAIEELTALKGIGPWTA 211
Query: 262 D 262
+
Sbjct: 212 E 212
Score = 42.8 bits (101), Expect = 2e-04
Identities = 13/77 (16%), Positives = 23/77 (29%), Gaps = 7/77 (9%)
Query: 327 GDFVADCICLMSLSHLQAVPVDTHVYQIACNHYHFQKSTSKTLTPAVYNQIRAFFADKFG 386
G + A+ L L P D + A + L + A+++G
Sbjct: 207 GPWTAEMFLLFGLGRPDVFPADDLGLRRAIKKLY-------RLPTRPTEKEVRELAERWG 259
Query: 387 KYAGWAHSILFCADLKK 403
Y +A L+
Sbjct: 260 PYRSYAALYLWRYARAT 276
>gnl|CDD|238013 cd00056, ENDO3c, endonuclease III; includes endonuclease III
(DNA-(apurinic or apyrimidinic site) lyase), alkylbase
DNA glycosidases (Alka-family) and other DNA
glycosidases.
Length = 158
Score = 59.6 bits (145), Expect = 1e-10
Identities = 31/141 (21%), Positives = 53/141 (37%), Gaps = 48/141 (34%)
Query: 129 ENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSHAKSCPAVTK 188
E + S + S ++ +++ + YG
Sbjct: 2 EVLVSEILSQQTTDKAVNKAYERLFERYG------------------------------- 30
Query: 189 FFAFPSIDALARPAVEAKLRQLGFG----YRAKFIQKSAEYIIQG-GGESWLERLGGKSY 243
P+ +ALA E +LR+L +AK++++ A I++G GG
Sbjct: 31 ----PTPEALAAADEE-ELRELIRSLGYRRKAKYLKELARAIVEGFGGLVL-------DD 78
Query: 244 EEAREELQRLPGIGAKVGDGV 264
+AREEL LPG+G K + V
Sbjct: 79 PDAREELLALPGVGRKTANVV 99
Score = 35.7 bits (83), Expect = 0.017
Identities = 17/72 (23%), Positives = 27/72 (37%), Gaps = 9/72 (12%)
Query: 327 GDFVADCICLMSLSHLQAVPVDTHVYQIACNHYHFQKSTSKTLTPAVYNQIRAFFADKFG 386
G A+ + L +L A PVDTHV ++ K + ++ +
Sbjct: 92 GRKTANVVLLFAL-GPDAFPVDTHVRRVLKRLGLIPKKKT-------PEELEELLEELLP 143
Query: 387 K-YAGWAHSILF 397
K Y G A+ L
Sbjct: 144 KPYWGEANQALM 155
>gnl|CDD|214684 smart00478, ENDO3c, endonuclease III. includes endonuclease III
(DNA-(apurinic or apyrimidinic site) lyase), alkylbase
DNA glycosidases (Alka-family) and other DNA
glycosidases.
Length = 149
Score = 51.1 bits (123), Expect = 8e-08
Identities = 25/85 (29%), Positives = 42/85 (49%), Gaps = 14/85 (16%)
Query: 183 CPAVTKFF-AFPSIDALA---RPAVEAKLRQLGFGY-RAKFIQKSAEYIIQGGGESWLER 237
A + F FP+ + LA +E +R LGF +A+++ + A ++ E
Sbjct: 11 NKATERLFEKFPTPEDLAAADEEELEELIRGLGFYRRKARYLIELARILV--------EE 62
Query: 238 LGGKSYEEAREELQRLPGIGAKVGD 262
GG+ + REEL +LPG+G K +
Sbjct: 63 YGGE-VPDDREELLKLPGVGRKTAN 86
Score = 35.7 bits (83), Expect = 0.016
Identities = 12/77 (15%), Positives = 24/77 (31%), Gaps = 10/77 (12%)
Query: 327 GDFVADCICLMSLSHLQAVPVDTHVYQIACNHYHFQKSTSKTLTPAVYNQIRAFFADKFG 386
G A+ + +L +PVDTHV +IA K + ++
Sbjct: 81 GRKTANAVLSFAL-GKPFIPVDTHVLRIAKRLGLVDK-------KSTPEEVEKLLEKLLP 132
Query: 387 K--YAGWAHSILFCADL 401
+ + ++
Sbjct: 133 EEDWRELNLLLIDFGRT 149
>gnl|CDD|216088 pfam00730, HhH-GPD, HhH-GPD superfamily base excision DNA repair
protein. This family contains a diverse range of
structurally related DNA repair proteins. The
superfamily is called the HhH-GPD family after its
hallmark Helix-hairpin-helix and Gly/Pro rich loop
followed by a conserved aspartate. This includes
endonuclease III, EC:4.2.99.18 and MutY an A/G-specific
adenine glycosylase, both have a C terminal 4Fe-4S
cluster. The family also includes 8-oxoguanine DNA
glycosylases. The methyl-CPG binding protein MBD4 also
contains a related domain that is a thymine DNA
glycosylase. The family also includes
DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other
members of the AlkA family.
Length = 144
Score = 45.0 bits (107), Expect = 1e-05
Identities = 25/88 (28%), Positives = 40/88 (45%), Gaps = 17/88 (19%)
Query: 184 PAVTKFFA---FPSIDALARPAVEAKLRQL----GF-GYRAKFIQKSAEYIIQG-GGESW 234
+ F FP+ + LA E +LR+L GF +AK+I++ A +++G G
Sbjct: 16 KITKRLFERYGFPTPEDLAEAD-EEELRELIKGLGFYRRKAKYIKELARILVEGYLGLVP 74
Query: 235 LERLGGKSYEEAREELQRLPGIGAKVGD 262
L+ E E L LPG+G +
Sbjct: 75 LD-------LEELEALLALPGVGRWTAE 95
Score = 28.9 bits (65), Expect = 3.2
Identities = 11/43 (25%), Positives = 16/43 (37%), Gaps = 1/43 (2%)
Query: 331 ADCICLMSLSHLQAVP-VDTHVYQIACNHYHFQKSTSKTLTPA 372
A+ + L +L P VDTHV ++A K
Sbjct: 94 AEAVLLFALGRPDVFPAVDTHVRRVAKRLGLIDTKPPKKEVER 136
>gnl|CDD|223255 COG0177, Nth, Predicted EndoIII-related endonuclease [DNA
replication, recombination, and repair].
Length = 211
Score = 40.6 bits (96), Expect = 6e-04
Identities = 25/87 (28%), Positives = 41/87 (47%), Gaps = 16/87 (18%)
Query: 184 PAVTKFFA-FPSIDALA---RPAVEAKLRQLGFGYR--AKFIQKSAEYIIQGGGESWLER 237
A F +P+ + L +E ++ +G YR AK I++ A ++ E+
Sbjct: 49 KATPALFKRYPTPEDLLNADEEELEELIKSIGL-YRNKAKNIKELARILL--------EK 99
Query: 238 LGGKSYEEAREELQRLPGIGAKVGDGV 264
GG+ + REEL LPG+G K + V
Sbjct: 100 FGGE-VPDTREELLSLPGVGRKTANVV 125
>gnl|CDD|224115 COG1194, MutY, A/G-specific DNA glycosylase [DNA replication,
recombination, and repair].
Length = 342
Score = 36.2 bits (84), Expect = 0.032
Identities = 26/72 (36%), Positives = 40/72 (55%), Gaps = 14/72 (19%)
Query: 191 AFPSIDALARPAVEAKLRQL--GFGY--RAKFIQKSAEYIIQGGGESWLERLGGKSYEEA 246
FP+I ALA A E ++ + G GY RA+ + K+A+ + +ER GG+ + +
Sbjct: 62 RFPTIKALAA-APEDEVLKAWEGLGYYSRARNLHKAAQEV--------VERHGGE-FPDD 111
Query: 247 REELQRLPGIGA 258
EEL LPG+G
Sbjct: 112 EEELAALPGVGP 123
>gnl|CDD|109681 pfam00633, HHH, Helix-hairpin-helix motif. The helix-hairpin-helix
DNA-binding motif is found to be duplicated in the
central domain of RuvA. The HhH domain of DisA, a
bacterial checkpoint control protein, is a DNA-binding
domain.
Length = 30
Score = 28.1 bits (64), Expect = 0.60
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 247 REELQRLPGIGAKVGDGVFK 266
REEL LPG+G K + +
Sbjct: 10 REELLALPGVGPKTAEAILS 29
>gnl|CDD|172427 PRK13910, PRK13910, DNA glycosylase MutY; Provisional.
Length = 289
Score = 31.5 bits (71), Expect = 0.90
Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 12/78 (15%)
Query: 191 AFPSIDALARPAVEAKL---RQLGFGYRAKFIQKSAEYIIQGGGESWLERLGGKSYEEAR 247
AFP++ LA +E L R LG+ RAK ++KSAE + +
Sbjct: 21 AFPTLKDLANAPLEEVLLLWRGLGYYSRAKNLKKSAEICV---------KEHHSQLPNDY 71
Query: 248 EELQRLPGIGAKVGDGVF 265
+ L +LPGIGA + +
Sbjct: 72 QSLLKLPGIGAYTANAIL 89
>gnl|CDD|113793 pfam05036, SPOR, Sporulation related domain. This 70 residue
domain is composed of two 35 residue repeats found in
proteins involved in sporulation and cell division such
as FtsN, DedD, and CwlM. This domain is involved in
binding peptidoglycan. Two tandem repeats fold into a
pseudo-2-fold symmetric single-domain structure
containing numerous contacts between the repeats. FtsN
is an essential cell division protein with a simple
bitopic topology, a short N-terminal cytoplasmic segment
fused to a large carboxy periplasmic domain through a
single transmembrane domain. These repeats lay at the
periplasmic C-terminus. FtsN localises to the septum
ring complex.
Length = 75
Score = 28.8 bits (65), Expect = 0.98
Identities = 20/54 (37%), Positives = 26/54 (48%), Gaps = 9/54 (16%)
Query: 205 AKLRQLGFGYRAKFIQKSAEYIIQGGGESWLERLGG-KSYEEAREELQRLPGIG 257
AKLR GF + E + GGG + R+G S EEAR L++L G
Sbjct: 23 AKLRAKGF--------AAKEAVTSGGGGLYRVRVGPFASREEARAALKKLKAAG 68
>gnl|CDD|223416 COG0339, Dcp, Zn-dependent oligopeptidases [Amino acid transport
and metabolism].
Length = 683
Score = 31.5 bits (72), Expect = 1.1
Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 7/71 (9%)
Query: 235 LERLGGKSYEEAREELQRLPGIGAKVGDGVFKEHVWTLWADPSYLHYQVYSQHKLNTNSV 294
L L K+ +A +EL L A+ G+ + W D +Y + Q K +
Sbjct: 301 LNDLAEKARPQAEKELAELQAFAAEEEGGLPELQPW----DWAYYAEK-QRQEKYAFD-- 353
Query: 295 ETMLKEYFRLD 305
E L+ YF L+
Sbjct: 354 EEELRPYFPLN 364
>gnl|CDD|233845 TIGR02395, rpoN_sigma, RNA polymerase sigma-54 factor. A sigma
factor is a DNA-binding protein protein that binds to
the DNA-directed RNA polymerase core to produce the
holoenzyme capable of initiating transcription at
specific sites. Different sigma factors act in
vegetative growth, heat shock, extracytoplasmic
functions (ECF), etc. This model represents the clade of
sigma factors called sigma-54, or RpoN (unrelated to
sigma 70-type factors such as RpoD/SigA). RpoN is
responsible for enhancer-dependent transcription, and
its presence characteristically is associated with
varied panels of activators, most of which are
enhancer-binding proteins (but see Brahmachary, et al.,
PMID:15231786). RpoN may be responsible for
transcription of nitrogen fixation genes, flagellins,
pilins, etc., and synonyms for the gene symbol rpoN,
such as ntrA, reflect these observations [Transcription,
Transcription factors].
Length = 429
Score = 30.7 bits (70), Expect = 1.5
Identities = 20/69 (28%), Positives = 29/69 (42%), Gaps = 13/69 (18%)
Query: 204 EAKLRQLGFGYRAKFIQKSAEYIIQG---GG------ESWLERLG--GKSYEEAREELQR 252
E L QL + + +K A YII G E + L + E+ E +QR
Sbjct: 80 EHLLEQLDLLFFTERDRKIALYIIDNLDEDGYLEIDLEEIADELEVSEEEVEKVLELIQR 139
Query: 253 L--PGIGAK 259
L G+GA+
Sbjct: 140 LDPAGVGAR 148
>gnl|CDD|236844 PRK11097, PRK11097, endo-1,4-D-glucanase; Provisional.
Length = 376
Score = 30.3 bits (69), Expect = 2.0
Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 11/45 (24%)
Query: 246 AREELQRLPGIG-----AKVGDGVFKE-HVWTLWADPSYLHYQVY 284
AREE+ +PG+G VG F + W L +PSYL Q+
Sbjct: 149 AREEVVTVPGLGSMLLPGPVG---FADDGSWRL--NPSYLPPQLL 188
>gnl|CDD|130155 TIGR01083, nth, endonuclease III. This equivalog model identifes
nth members of the pfam00730 superfamily (HhH-GPD:
Helix-hairpin-helix and Gly/Pro rich loop followed by a
conserved aspartate). The major members of the
superfamily are nth and mutY [DNA metabolism, DNA
replication, recombination, and repair].
Length = 191
Score = 29.6 bits (67), Expect = 2.6
Identities = 30/86 (34%), Positives = 40/86 (46%), Gaps = 17/86 (19%)
Query: 181 KSCPAVTK--FFAFPSIDALA---RPAVEAKLRQLGFGYR--AKFIQKSAEYIIQGGGES 233
KS TK F +P+ ALA +E ++ +G YR AK I ++
Sbjct: 42 KSVNKATKKLFEVYPTPQALAQAGLEELEEYIKSIGL-YRNKAKNIIALCRILV------ 94
Query: 234 WLERLGGKSYEEAREELQRLPGIGAK 259
ER GG E REEL +LPG+G K
Sbjct: 95 --ERYGG-EVPEDREELVKLPGVGRK 117
>gnl|CDD|130187 TIGR01117, mmdA, methylmalonyl-CoA decarboxylase alpha subunit.
This model describes methymalonyl-CoA decarboxylase
aplha subunit in archaea and bacteria. Metylmalonyl-CoA
decarboxylase Na+ pump is a representative of a class of
Na+ transport decarboxylases that couples the energy
derived by decarboxylation of carboxylic acid substrates
to drive the extrusion of Na+ ion across the membrane
[Energy metabolism, ATP-proton motive force
interconversion, Energy metabolism, Fermentation,
Transport and binding proteins, Cations and iron
carrying compounds].
Length = 512
Score = 29.8 bits (67), Expect = 3.3
Identities = 17/50 (34%), Positives = 24/50 (48%)
Query: 219 IQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAKVGDGVFKEH 268
+ + E I QGGGE +E+ + ARE L L G+ V F +H
Sbjct: 6 LHEKKEKIKQGGGEKRIEKQHAQGKMTARERLALLFDPGSFVEIDQFVKH 55
>gnl|CDD|140318 PTZ00297, PTZ00297, pantothenate kinase; Provisional.
Length = 1452
Score = 30.2 bits (68), Expect = 3.3
Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 2/64 (3%)
Query: 239 GGKSYEEAREELQRLPGIGAKVGDGVFKEHVWTLWADPSYLHYQVYSQHKLNTNSVETML 298
GG + +E L L +G+ V + ++ E P L + Q KL S
Sbjct: 214 GGHPTKRFQELLNELQDLGSGVREVIYDETGQHPPTRPPILFFP--EQSKLERYSSTPQR 271
Query: 299 KEYF 302
++YF
Sbjct: 272 QDYF 275
>gnl|CDD|165023 PHA02641, PHA02641, hypothetical protein; Provisional.
Length = 188
Score = 28.8 bits (64), Expect = 4.2
Identities = 23/99 (23%), Positives = 45/99 (45%), Gaps = 21/99 (21%)
Query: 80 NSVETMLKEYFR----------LDENLPELYAEWSNRDAFFRQTCGD-----FVGIRMLN 124
+S+E +L++YF L +N+ +LY + + D F ++ GD +++
Sbjct: 58 DSLENVLEDYFAWRAHISKIDILPKNVGKLYLDLMDLDTFAKKMMGDLDILILDVLKLDE 117
Query: 125 QDLTENIFSFLCSSNNNIAR------ISGMIDKMCKEYG 157
QD +F+F+ S + N + G I +C +G
Sbjct: 118 QDADVRLFNFISSMDINFNNCDTCLILIGFIGYVCSFWG 156
>gnl|CDD|220499 pfam09979, DUF2213, Uncharacterized protein conserved in bacteria
(DUF2213). Members of this family of bacterial proteins
comprise various hypothetical and phage-related
proteins. The exact function of these proteins has not,
as yet, been determined.
Length = 170
Score = 28.1 bits (63), Expect = 6.4
Identities = 11/35 (31%), Positives = 14/35 (40%)
Query: 196 DALARPAVEAKLRQLGFGYRAKFIQKSAEYIIQGG 230
DA A +E R+L GY A + Q Q
Sbjct: 106 DAAAIALIEDGKRELSCGYDADYDQTPGVTDGQPY 140
>gnl|CDD|213851 TIGR03700, mena_SCO4494, putative menaquinone biosynthesis protein,
SCO4494 family. Members of this protein family appear
to be involved in menaquinone biosynthesis by an
alternate pathway via futalosine, based on close
phylogenetic correlation with known markers of the
futalosine pathway, gene clustering in many organisms,
and paralogy with the SCO4550 protein [Biosynthesis of
cofactors, prosthetic groups, and carriers, Menaquinone
and ubiquinone].
Length = 351
Score = 28.9 bits (65), Expect = 6.4
Identities = 18/88 (20%), Positives = 32/88 (36%), Gaps = 22/88 (25%)
Query: 234 WLERLGGKSYEEAREELQR-----LPGIGAKVGDGVFKEHV------WTLWADPSYLHYQ 282
++ G EE +EL+ +PG GA++ ++ + W +H
Sbjct: 140 HFSKISGLPTEEVLDELKEAGLDSMPGGGAEIFAEEVRQQICPEKISAERW---LEIHRT 196
Query: 283 VYSQHKLNTNSVETML-----KEYFRLD 305
H+L + TML R+D
Sbjct: 197 A---HELGLKTNATMLYGHIETPAHRVD 221
>gnl|CDD|165574 PHA03330, PHA03330, putative primase; Provisional.
Length = 771
Score = 28.9 bits (64), Expect = 7.6
Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 6/58 (10%)
Query: 236 ERLGGKSYEEAREELQRLPGIGAKVGDGVFKEHV----WTLWADPSYLHYQVYSQHKL 289
E LGG YE+A E + G ++ V K+ + L P H + S H+
Sbjct: 160 EHLGGAHYEDAVEAERAFAGPKCQILRNVQKQKLAGFDSRL--IPELFHDLLLSIHEE 215
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
0.320 0.135 0.417
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: 23,523,825
Number of extensions: 2268377
Number of successful extensions: 2100
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2086
Number of HSP's successfully gapped: 32
Length of query: 457
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 357
Effective length of database: 6,502,202
Effective search space: 2321286114
Effective search space used: 2321286114
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 (21.8 bits)
S2: 61 (27.2 bits)