RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16216
(129 letters)
>gnl|CDD|176456 cd01702, PolY_Pol_eta, DNA Polymerase eta. Pol eta, also called
Rad30A, is a translesion synthesis (TLS) polymerase.
Translesion synthesis is a process that allows the
bypass of a variety of DNA lesions. TLS polymerases
lack proofreading activity and have low fidelity and low
processivity. They use damaged DNA as templates and
insert nucleotides opposite the lesions. Unlike other
Y-family members, Pol eta can efficiently and accurately
replicate DNA past UV-induced lesions. Its activity is
initiated by two simultaneous interactions: the PIP box
in pol eta interacting with PCNA, and the UBZ
(ubiquitin-binding zinc finger) in pol eta interacting
with monoubiquitin attached to PCNA. Pol eta is more
efficient in copying damaged DNA than undamaged DNA and
seems to recognize when a lesion has been passed,
facilitating a lesion-dependent dissociation from the
DNA.
Length = 359
Score = 58.9 bits (143), Expect = 3e-11
Identities = 18/40 (45%), Positives = 29/40 (72%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMK 40
YR A R+++ +L F ++VE+ASIDEAY+DL + E ++
Sbjct: 94 YRRASRKILNILKRFGDVVEKASIDEAYLDLGSRIVEEIR 133
Score = 42.7 bits (101), Expect = 1e-05
Identities = 17/32 (53%), Positives = 21/32 (65%)
Query: 97 LAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128
L + IVEEIR V + + CSAGIAHNK+
Sbjct: 122 LDLGSRIVEEIRQQVYDELGYTCSAGIAHNKM 153
>gnl|CDD|176459 cd03586, PolY_Pol_IV_kappa, DNA Polymerase IV/Kappa. Pol IV, also
known as Pol kappa, DinB, and Dpo4, is a translesion
synthesis (TLS) polymerase. Translesion synthesis is a
process that allows the bypass of a variety of DNA
lesions. TLS polymerases lack proofreading activity and
have low fidelity and low processivity. They use
damaged DNA as templates and insert nucleotides opposite
the lesions. Known primarily as Pol IV in prokaryotes
and Pol kappa in eukaryotes, this polymerase has a
propensity for generating frameshift mutations. The
eukaryotic Pol kappa differs from Pol IV and Dpo4 by an
N-terminal extension of ~75 residues known as the
"N-clasp" region. The structure of Pol kappa shows DNA
that is almost totally encircled by Pol kappa, with the
N-clasp region augmenting the interactions between DNA
and the polymerase. Pol kappa is more resistant than Pol
eta and Pol iota to bulky guanine adducts and is
efficient at catalyzing the incorporation of dCTP.
Bacterial pol IV has a higher error rate than other
Y-family polymerases.
Length = 334
Score = 53.3 bits (129), Expect = 3e-09
Identities = 20/47 (42%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAA 47
YR R+++ +L E++ +VE SIDEAY+D+TD V S IA
Sbjct: 74 YREVSRQIMEILREYTPLVEPLSIDEAYLDVTDYVRLF-GSATEIAK 119
Score = 42.1 bits (100), Expect = 2e-05
Identities = 15/38 (39%), Positives = 20/38 (52%)
Query: 91 TEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128
T+ + A I +EIRA + +T SAGIA NK
Sbjct: 105 TDYVRLFGSATEIAKEIRARIREETGLTASAGIAPNKF 142
>gnl|CDD|179337 PRK01810, PRK01810, DNA polymerase IV; Validated.
Length = 407
Score = 51.2 bits (123), Expect = 1e-08
Identities = 17/36 (47%), Positives = 25/36 (69%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVH 36
YR A R++ +LSEF+ +V+ SIDE Y+D+TD
Sbjct: 83 YREASRQMFQILSEFTPLVQPVSIDEGYLDITDCYA 118
Score = 26.5 bits (59), Expect = 4.5
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 103 IVEEIRAAVLSKTQFHCSAGIAHNK 127
I + I+ +L++ Q CS GIA NK
Sbjct: 125 IAKMIQQRLLTELQLPCSIGIAPNK 149
>gnl|CDD|216135 pfam00817, IMS, impB/mucB/samB family. These proteins are involved
in UV protection.
Length = 148
Score = 45.7 bits (109), Expect = 4e-07
Identities = 29/129 (22%), Positives = 39/129 (30%), Gaps = 60/129 (46%)
Query: 1 YRNAGREVIAVLSEF-SNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFG 59
YR A R + +L F VE SIDEA++DL
Sbjct: 72 YRRASRRIAEILRRFSPPKVEVYSIDEAFLDL---------------------------- 103
Query: 60 PDNNDEDARKAGVMEWLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHC 119
T L + LA + +R A+ +T C
Sbjct: 104 -------------------------TGLERLFGGEEALA------KRLRRAIAEETGLTC 132
Query: 120 SAGIAHNKV 128
S GIA NK+
Sbjct: 133 SIGIAPNKL 141
>gnl|CDD|223466 COG0389, DinP, Nucleotidyltransferase/DNA polymerase involved in
DNA repair [DNA replication, recombination, and repair].
Length = 354
Score = 46.5 bits (111), Expect = 5e-07
Identities = 17/36 (47%), Positives = 25/36 (69%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVH 36
YR A E+ A+L ++ +VE SIDEA++DLTD +
Sbjct: 77 YRLASAEIRAILERYTPLVEPLSIDEAFLDLTDALR 112
Score = 33.8 bits (78), Expect = 0.015
Identities = 13/32 (40%), Positives = 16/32 (50%)
Query: 97 LAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128
LA A I EIR +L + S GI+ NK
Sbjct: 116 LADAPRIALEIRFGILLELGLTASVGISDNKF 147
>gnl|CDD|176453 cd00424, PolY, Y-family of DNA polymerases. Y-family DNA
polymerases are a specialized subset of polymerases that
facilitate translesion synthesis (TLS), a process that
allows the bypass of a variety of DNA lesions. Unlike
replicative polymerases, TLS polymerases lack
proofreading activity and have low fidelity and low
processivity. They use damaged DNA as templates and
insert nucleotides opposite the lesions. The active
sites of TLS polymerases are large and flexible to allow
the accomodation of distorted bases. Most TLS
polymerases are members of the Y-family, including Pol
eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is
found exclusively in bacteria. In eukaryotes, the
B-family polymerase Pol zeta also functions as a TLS
polymerase. Expression of Y-family polymerases is often
induced by DNA damage and is believed to be highly
regulated. TLS is likely induced by the
monoubiquitination of the replication clamp PCNA, which
provides a scaffold for TLS polymerases to bind in order
to access the lesion. Because of their high error
rates, TLS polymerases are potential targets for cancer
treatment and prevention.
Length = 343
Score = 45.4 bits (108), Expect = 1e-06
Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 14/62 (22%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVH---------ERMKS-----IGHIA 46
YR +++ L E + +VE ASIDE ++DLT R+K +G I
Sbjct: 75 YRRLSERLLSELEEVAPLVEVASIDELFLDLTGSARLLGLGSEVALRIKRHIAEQLGGIT 134
Query: 47 AS 48
AS
Sbjct: 135 AS 136
>gnl|CDD|235035 PRK02406, PRK02406, DNA polymerase IV; Validated.
Length = 343
Score = 41.3 bits (98), Expect = 4e-05
Identities = 11/36 (30%), Positives = 23/36 (63%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVH 36
Y+ R++ + +++++E S+DEAY+D+TD
Sbjct: 71 YKEVSRQIREIFRRYTDLIEPLSLDEAYLDVTDNKL 106
Score = 36.6 bits (86), Expect = 0.001
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 91 TEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNK 127
T++ + A +I +EIR + + SAG+A NK
Sbjct: 102 TDNKLCIGSATLIAQEIRQDIFEELGLTASAGVAPNK 138
>gnl|CDD|184529 PRK14133, PRK14133, DNA polymerase IV; Provisional.
Length = 347
Score = 40.5 bits (95), Expect = 7e-05
Identities = 14/34 (41%), Positives = 23/34 (67%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDV 34
Y+ + + +L E + IVE SIDEAY+D+T++
Sbjct: 79 YKEVSKNIFKILYEVTPIVEPVSIDEAYLDITNI 112
>gnl|CDD|179251 PRK01216, PRK01216, DNA polymerase IV; Validated.
Length = 351
Score = 39.0 bits (91), Expect = 2e-04
Identities = 15/35 (42%), Positives = 24/35 (68%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVV 35
Y+ ++ +L E+S +E ASIDEAY+D++D V
Sbjct: 81 YQQVSNRIMKLLREYSEKIEIASIDEAYLDISDKV 115
>gnl|CDD|179564 PRK03352, PRK03352, DNA polymerase IV; Validated.
Length = 346
Score = 38.5 bits (90), Expect = 3e-04
Identities = 19/39 (48%), Positives = 24/39 (61%), Gaps = 6/39 (15%)
Query: 91 TEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVK 129
T+D + LA EEIRAAVL +T CS GI NK++
Sbjct: 117 TDDPEALA------EEIRAAVLERTGLSCSVGIGDNKLR 149
Score = 26.5 bits (59), Expect = 3.9
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYI 29
Y A EV+A L + VE DEA++
Sbjct: 85 YDAASEEVMATLRDLGVPVEVWGWDEAFL 113
>gnl|CDD|179473 PRK02794, PRK02794, DNA polymerase IV; Provisional.
Length = 419
Score = 37.6 bits (88), Expect = 7e-04
Identities = 15/32 (46%), Positives = 22/32 (68%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLT 32
Y GREV A++ + +VE SIDEA++DL+
Sbjct: 111 YVRVGREVRAMMQALTPLVEPLSIDEAFLDLS 142
>gnl|CDD|179607 PRK03609, umuC, DNA polymerase V subunit UmuC; Reviewed.
Length = 422
Score = 36.7 bits (85), Expect = 0.001
Identities = 24/65 (36%), Positives = 32/65 (49%), Gaps = 5/65 (7%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHER-MKSIGH-IAASQLSNTFV--- 55
Y + V++ L E S VE SIDEA+ DLT V + R + G I A+ L T +
Sbjct: 77 YADMSNRVMSTLEELSPRVEIYSIDEAFCDLTGVRNCRDLTDFGREIRATVLQRTHLTVG 136
Query: 56 VGFGP 60
VG
Sbjct: 137 VGIAQ 141
>gnl|CDD|179663 PRK03858, PRK03858, DNA polymerase IV; Validated.
Length = 396
Score = 36.5 bits (85), Expect = 0.002
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLT 32
Y A + V V + + +VE SIDEA++D+
Sbjct: 76 YSRASKAVFEVFRDTTPLVEGLSIDEAFLDVG 107
>gnl|CDD|176454 cd01700, PolY_Pol_V_umuC, umuC subunit of DNA Polymerase V. umuC
subunit of Pol V. Pol V is a bacterial translesion
synthesis (TLS) polymerase that consists of the
heterotrimer of one umuC and two umuD subunits.
Translesion synthesis is a process that allows the
bypass of a variety of DNA lesions. TLS polymerases
lack proofreading activity and have low fidelity and low
processivity. They use damaged DNA as templates and
insert nucleotides opposite the lesions. Pol V, RecA,
single stranded DNA-binding protein, beta sliding clamp,
and gamma clamp loading complex are responsible for
inducing the SOS response in bacteria to repair
UV-induced DNA damage.
Length = 344
Score = 35.6 bits (83), Expect = 0.003
Identities = 13/28 (46%), Positives = 20/28 (71%)
Query: 6 REVIAVLSEFSNIVERASIDEAYIDLTD 33
R ++++L FS VE SIDE+++DLT
Sbjct: 80 RRIMSILERFSPDVEVYSIDESFLDLTG 107
Score = 29.1 bits (66), Expect = 0.55
Identities = 7/26 (26%), Positives = 12/26 (46%)
Query: 103 IVEEIRAAVLSKTQFHCSAGIAHNKV 128
+ +IR +L +T + GI K
Sbjct: 117 LARKIRRRILQETGIPVTVGIGPTKT 142
>gnl|CDD|176455 cd01701, PolY_Rev1, DNA polymerase Rev1. Rev1 is a translesion
synthesis (TLS) polymerase found in eukaryotes.
Translesion synthesis is a process that allows the
bypass of a variety of DNA lesions. TLS polymerases
lack proofreading activity and have low fidelity and low
processivity. They use damaged DNA as templates and
insert nucleotides opposite the lesions. Rev1 has both
structural and enzymatic roles. Structurally, it is
believed to interact with other nonclassical polymerases
and replication machinery to act as a scaffold.
Enzymatically, it catalyzes the specific insertion of
dCMP opposite abasic sites. Rev1 interacts with the
Rev7 subunit of the B-family TLS polymerase Pol zeta
(Rev3/Rev7). Rev1 is known to actively promote the
introduction of mutations, potentially making it a
significant target for cancer treatment.
Length = 404
Score = 35.8 bits (83), Expect = 0.003
Identities = 15/50 (30%), Positives = 19/50 (38%), Gaps = 6/50 (12%)
Query: 79 VYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKV 128
D + L E E +ELA E IR + T S GI N +
Sbjct: 150 ALIDITSLLEETYELPEELA------EAIRNEIRETTGCSASVGIGPNIL 193
Score = 27.7 bits (62), Expect = 1.7
Identities = 10/27 (37%), Positives = 19/27 (70%)
Query: 11 VLSEFSNIVERASIDEAYIDLTDVVHE 37
+L+ +++ +E S DEA ID+T ++ E
Sbjct: 134 ILASYTDNIEAVSCDEALIDITSLLEE 160
>gnl|CDD|235118 PRK03348, PRK03348, DNA polymerase IV; Provisional.
Length = 454
Score = 35.3 bits (82), Expect = 0.004
Identities = 14/30 (46%), Positives = 19/30 (63%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYID 30
YR A R V L E S +VE+ S DEA+++
Sbjct: 82 YRAASRRVFDTLRELSPVVEQLSFDEAFVE 111
>gnl|CDD|176457 cd01703, PolY_Pol_iota, DNA Polymerase iota. Pol iota, also called
Rad30B, is a translesion synthesis (TLS) polymerase.
Translesion synthesis is a process that allows the
bypass of a variety of DNA lesions. TLS polymerases
lack proofreading activity and have low fidelity and low
processivity. They use damaged DNA as templates and
insert nucleotides opposite the lesions. Pol iota is
thought to be one of the least efficient polymerases,
particularly when opposite pyrimidines; it can
incorporate the correct nucleotide opposite a purine
much more efficiently than opposite a pyrimidine, and
prefers to insert guanosine instead of adenosine
opposite thymidine. Pol iota is believed to use
Hoogsteen rather than Watson-Crick base pairing, which
may explain the varying efficiency for different
template nucleotides.
Length = 379
Score = 31.3 bits (71), Expect = 0.098
Identities = 16/58 (27%), Positives = 31/58 (53%), Gaps = 8/58 (13%)
Query: 1 YRNAGREVIAVLSEFS--NIVERASIDEAYIDLTDVVHERMKSIGHIAA---SQLSNT 53
+R+ ++V +L +S + VER DE ++D+T++ R+ HIA ++ N
Sbjct: 72 FRDMSKKVYRLLRSYSWNDRVERLGFDENFMDVTEM---RLLVASHIAYEMRERIENE 126
Score = 29.7 bits (67), Expect = 0.37
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 84 DTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNK 127
D + M+ TE L +A I E+R + ++ C AGIA NK
Sbjct: 98 DENFMDVTE--MRLLVASHIAYEMRERIENELGLTCCAGIASNK 139
>gnl|CDD|235104 PRK03103, PRK03103, DNA polymerase IV; Reviewed.
Length = 409
Score = 31.1 bits (71), Expect = 0.12
Identities = 10/29 (34%), Positives = 19/29 (65%)
Query: 8 VIAVLSEFSNIVERASIDEAYIDLTDVVH 36
+ +L +F+++VE SIDE ++D+T
Sbjct: 88 ITRILEDFTDLVEPFSIDEQFLDVTGSQK 116
>gnl|CDD|188237 TIGR02634, xylF, D-xylose ABC transporter, substrate-binding
protein. Members of this family are periplasmic (when
in Gram-negative bacteria) binding proteins for D-xylose
import by a high-affinity ATP-binding cassette (ABC)
transporter [Transport and binding proteins,
Carbohydrates, organic alcohols, and acids].
Length = 302
Score = 28.3 bits (63), Expect = 1.0
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 2/73 (2%)
Query: 4 AGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNN 63
A E I VL+ + ++ A ID Y+ + M++ +AA+ N F++G P +N
Sbjct: 75 AKDEGIKVLA-YDRLINDADID-FYLSFDNEKVGEMQAKAVLAAAPKGNYFLMGGSPTDN 132
Query: 64 DEDARKAGVMEWL 76
+ + G M+ L
Sbjct: 133 NAKLLRGGQMKVL 145
>gnl|CDD|240277 PTZ00118, PTZ00118, 40S ribosomal protein S4; Provisional.
Length = 262
Score = 27.5 bits (61), Expect = 1.7
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 33 DVVHERMKSIGHIAASQLSNTFVVGFGPDN 62
D++H + S G A++LSN FV+G G
Sbjct: 206 DLIHVK-DSRGKTFATRLSNVFVIGVGTKP 234
>gnl|CDD|234092 TIGR03023, WcaJ_sugtrans, Undecaprenyl-phosphate glucose
phosphotransferase. This family of proteins encompasses
the E. coli WcaJ protein involved in colanic acid
biosynthesis , the Methylobacillus EpsB protein involved
in methanolan biosynthesis , as well as the GumD protein
involved in the biosynthesis of xanthan. All of these
are closely related to the well-characterized WbaP
(formerly RfbP) protein which is the first enzyme in
O-antigen biosynthesis in Salmonella typhimurium. The
enzyme transfers galactose from UDP-galactose (NOTE: not
glucose) to a polyprenyl carrier (utilizing the highly
conserved C-terminal sugar transferase domain,
pfam02397) a reaction which takes place at the
cytoplasmic face of the inner membrane. The N-terminal
hydrophobic domain is then believed to facilitate the
"flippase" function of transferring the liposaccharide
unit from the cytoplasmic face to the periplasmic face
of the inner membrane. Most of these genes are found
within large operons dedicated to the production of
complex exopolysaccharides such as the enterobacterial
O-antigen. Colanic acid biosynthesis utilizes a
glucose-undecaprenyl carrier , knockout of EpsB
abolishes incorporation of UDP-glucose into the lipid
phase and the C-terminal portion of GumD has been shown
to be responsible for the glucosyl-1-transferase
activity.
Length = 451
Score = 27.5 bits (62), Expect = 1.9
Identities = 14/60 (23%), Positives = 23/60 (38%), Gaps = 5/60 (8%)
Query: 3 NAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFV-VGFGPD 61
G V+ L + ++ +DE YI L +R+ + L + V V PD
Sbjct: 171 VRGVPVLGKLDDLEELIREGEVDEVYIALPLAAEKRILEL----LDALEDLTVDVRLVPD 226
>gnl|CDD|236367 PRK09047, PRK09047, RNA polymerase factor sigma-70; Validated.
Length = 161
Score = 27.2 bits (61), Expect = 1.9
Identities = 16/59 (27%), Positives = 25/59 (42%), Gaps = 6/59 (10%)
Query: 52 NTFVVGFGPDNNDEDARKAGVMEWLGQVYSDTDTSLMENTEDFQELAIAG-VIVEEIRA 109
NT+V F ++D+D +E L D+ E+ D E A +I E I+
Sbjct: 53 NTWVSLFSSFSDDDDDDDFDPLETL-----DSADEGAESPADKLERAQVLQLIEEAIQK 106
>gnl|CDD|215431 PLN02801, PLN02801, beta-amylase.
Length = 517
Score = 27.1 bits (60), Expect = 3.3
Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 3/28 (10%)
Query: 78 QVYSDTDTSLMENTEDFQELAIAGVIVE 105
++YSD S EN DF E AGVI++
Sbjct: 156 EMYSDYMKSFRENMADFLE---AGVIID 180
>gnl|CDD|226107 COG3579, PepC, Aminopeptidase C [Amino acid transport and
metabolism].
Length = 444
Score = 27.1 bits (60), Expect = 3.4
Identities = 15/56 (26%), Positives = 22/56 (39%), Gaps = 8/56 (14%)
Query: 39 MKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVYSDTDTSLMENTEDF 94
M+ + +A Q+ V FG D RK G+M DTD E++
Sbjct: 297 MERLKKLAIKQMQAGETVWFGCDVGQLSDRKTGIM--------DTDIYDYESSLGI 344
>gnl|CDD|218529 pfam05273, Pox_RNA_Pol_22, Poxvirus RNA polymerase 22 kDa
subunit. This family consists of several poxvirus
DNA-dependent RNA polymerase 22 kDa subunits.
Length = 185
Score = 26.2 bits (58), Expect = 4.4
Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 2/55 (3%)
Query: 10 AVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNND 64
AV+S +++ R D Y DL ++ K Q+ N V + P +D
Sbjct: 25 AVIS--KDVLLRYDTDVEYGDLVTIITVTHKIDNSKTVFQVFNESSVNYSPVEDD 77
>gnl|CDD|177670 PLN00036, PLN00036, 40S ribosomal protein S4; Provisional.
Length = 261
Score = 26.2 bits (58), Expect = 4.7
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 13/58 (22%)
Query: 2 RNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFG 59
RN GR + V I R E + +++H + + GH A++L N FV+G G
Sbjct: 187 RNRGR--VGV------IKNR----EKHKGSFEIIHVK-DATGHEFATRLGNVFVIGKG 231
>gnl|CDD|218707 pfam05704, Caps_synth, Capsular polysaccharide synthesis protein.
This family consists of several capsular polysaccharide
proteins. Capsular polysaccharide (CPS) is a major
virulence factor in Streptococcus pneumoniae.
Length = 279
Score = 26.1 bits (58), Expect = 5.6
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 10/49 (20%)
Query: 3 NAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLS 51
G EVI +L++ NI Y+D+ D + E+ +S G I+ + S
Sbjct: 76 APGYEVI-LLTK-DNI-------SEYVDIPDFIIEKFES-GKISRAHFS 114
>gnl|CDD|215623 PLN03190, PLN03190, aminophospholipid translocase; Provisional.
Length = 1178
Score = 26.0 bits (57), Expect = 6.9
Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 3/38 (7%)
Query: 68 RKAGVMEWLGQ---VYSDTDTSLMENTEDFQELAIAGV 102
R + E LGQ V+SD +L EN +FQ +I GV
Sbjct: 442 RALNINEDLGQIKYVFSDKTGTLTENKMEFQCASIWGV 479
>gnl|CDD|236784 PRK10876, recB, exonuclease V subunit beta; Provisional.
Length = 1181
Score = 26.1 bits (58), Expect = 6.9
Identities = 11/37 (29%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 90 NTEDFQELAIAGVIVEEIRA--AVLSKTQFHCSAGIA 124
E+ LA + E++R L+++ +HCS G+A
Sbjct: 782 AAEESVALAEEERLAEDLRLLYVALTRSVWHCSLGVA 818
>gnl|CDD|223157 COG0079, HisC, Histidinol-phosphate/aromatic aminotransferase and
cobyric acid decarboxylase [Amino acid transport and
metabolism].
Length = 356
Score = 25.7 bits (57), Expect = 7.3
Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 4/28 (14%)
Query: 6 REVIAVLSEFSNIVERASIDEAYIDLTD 33
R ++ L E +V IDEAYI+ +
Sbjct: 168 RALLEALPEGGLVV----IDEAYIEFSP 191
>gnl|CDD|132491 TIGR03450, mycothiol_INO1, inositol 1-phosphate synthase,
Actinobacterial type. This enzyme, inositol 1-phosphate
synthase as found in Actinobacteria, produces an
essential precursor for several different products,
including mycothiol, which is a glutathione analog, and
phosphatidylinositol, which is a phospholipid.
Length = 351
Score = 25.7 bits (56), Expect = 8.1
Identities = 26/103 (25%), Positives = 46/103 (44%), Gaps = 9/103 (8%)
Query: 14 EFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDE--DARKAG 71
+F N++ER ++ I T V ++ L + V GP ++ D RK
Sbjct: 220 DFKNMLERDRLESKKISKTQAV------TSNLPDRPLKDK-NVHIGPSDHVGWLDDRKWA 272
Query: 72 VMEWLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSK 114
+ G+ + D +L E + AGVI++ +RAA ++K
Sbjct: 273 YVRLEGRAFGDVPLNLEYKLEVWDSPNSAGVIIDAVRAAKIAK 315
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
0.316 0.131 0.362
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,635,269
Number of extensions: 589019
Number of successful extensions: 550
Number of sequences better than 10.0: 1
Number of HSP's gapped: 549
Number of HSP's successfully gapped: 60
Length of query: 129
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 43
Effective length of database: 7,123,158
Effective search space: 306295794
Effective search space used: 306295794
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.2 bits)