RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16215
(1041 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 = 232 bits (595), Expect = 2e-68
Identities = 107/241 (44%), Positives = 139/241 (57%), Gaps = 5/241 (2%)
Query: 185 LAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSMLYAN 244
L + IVEEIR V + + CSAGIAHNK+LAKL G++KP Q+IL +V+ ++
Sbjct: 122 LDLGSRIVEEIRQQVYDELGYTCSAGIAHNKMLAKLASGMNKPNAQTILRNDAVASFLSS 181
Query: 245 LSIKKVRHLGGKLGDEVVETLQCSTMLELEKF--SLKQLQSHFEEKTASWLYYIARGIDH 302
L I +R LGGKLG+E+++ L T ++ F S LQ HF EK WLY + RGIDH
Sbjct: 182 LPITSIRGLGGKLGEEIIDLLGLPTEGDVAGFRSSESDLQEHFGEKLGEWLYNLLRGIDH 241
Query: 303 EPVNARLVSKSIGCCKRFPGKTCLATRQDVSHWIQELADEVCERLEDDLTLNKRRAQLLT 362
EPV R + KS+G K FPGKT L+T +DV HW+ LA E+ RLEDD N RR + L
Sbjct: 242 EPVKPRPLPKSMGSSKNFPGKTALST-EDVQHWLLVLASELNSRLEDDRYENNRRPKTLV 300
Query: 363 VSFTQETDGKVNSCSRSIALASYKLQDIVEVSMQVINKTNSAPPISDLTPPLLFLGLSAS 422
+S Q G SRS AL Y Q IV+ + ++I N PL L LS +
Sbjct: 301 LSLRQ--RGDGVRRSRSCALPRYDAQKIVKDAFKLIKAINEEGLGLAWNYPLTLLSLSFT 358
Query: 423 K 423
K
Sbjct: 359 K 359
Score = 164 bits (417), Expect = 2e-44
Identities = 56/138 (40%), Positives = 76/138 (55%), Gaps = 21/138 (15%)
Query: 7 ALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAK 66
A IDMD F+ QVE L P+AVVQ+N IIAV+Y AR GVTR M DEAK
Sbjct: 1 AHIDMDAFFAQVEQVRLGLLRNDPVAVVQWN-----SIIAVSYAARAFGVTRFMTIDEAK 55
Query: 67 QHCPEIELCRVPSV----------------RGKADISKYRNAGREVIAVLSEFSNIVERA 110
+ CP++ L V + R K + YR A R+++ +L F ++VE+A
Sbjct: 56 KKCPDLILAHVATYKKGEDEADYHENPSPARHKVSLDPYRRASRKILNILKRFGDVVEKA 115
Query: 111 SIDEAYIDLTDVVHERMK 128
SIDEAY+DL + E ++
Sbjct: 116 SIDEAYLDLGSRIVEEIR 133
>gnl|CDD|223466 COG0389, DinP, Nucleotidyltransferase/DNA polymerase involved in
DNA repair [DNA replication, recombination, and repair].
Length = 354
Score = 172 bits (438), Expect = 4e-47
Identities = 110/401 (27%), Positives = 165/401 (41%), Gaps = 81/401 (20%)
Query: 4 RIIALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGD 63
R I +DMD FY VE + NP L GKP+ V G ++A +YEAR GV M
Sbjct: 1 RKILHVDMDAFYASVEERDNPELKGKPVVVGGGAPR--GVVLAASYEARAFGVRSAMPLF 58
Query: 64 EAKQHCPEIELCRVPSVRGKADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVV 123
EA + CP P A YR A E+ A+L ++ +VE SIDEA++DLTD +
Sbjct: 59 EALKLCPRA--IVAPP-NFAA----YRLASAEIRAILERYTPLVEPLSIDEAFLDLTDAL 111
Query: 124 HERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVYSDTDTSLMENTEDFQ 183
DA +
Sbjct: 112 RLL------------------------GLADAPRIA------------------------ 123
Query: 184 ELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSMLYA 243
L I I+ E+ S GI+ NK LAK+ L+KP +++ V L
Sbjct: 124 -LEIRFGILLELG--------LTASVGISDNKFLAKIASDLNKPDGITVIEPEEVPALLW 174
Query: 244 NLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGIDHE 303
L + + + GK+ E + L ST+ +L + L L+ F + LY +ARGID+
Sbjct: 175 QLPVLEFWGV-GKVTAEKLRRLGISTIGDLAETDLDALKKRFGKLGE-RLYRLARGIDNR 232
Query: 304 PVNA-RLVSKSIGCCKRFPGKTCLATRQDVSHWIQELADEVCERLEDDLT--LNKRRAQL 360
PV L +KSIG F +D++ +EL + + RL +++ L K
Sbjct: 233 PVREQALRAKSIGAESTFE--------EDLTDA-EELIERLRARLGEEVVSRLRKSGRHG 283
Query: 361 LTVSFTQET-DGKVNSCSRSIALASYKLQDIVEVSMQVINK 400
TVS +T D N+ SR +A + +I ++ ++
Sbjct: 284 RTVSVKLKTADFPTNTRSRKLAQPTSDPIEIYAAALPLLPP 324
>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 = 161 bits (409), Expect = 2e-43
Identities = 93/388 (23%), Positives = 147/388 (37%), Gaps = 74/388 (19%)
Query: 9 IDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAKQH 68
ID D F+ VE P L G+P+ VV +N+ +IA +YEAR GV R M EA++
Sbjct: 3 IDFDNFFASVEQLARPELKGRPVVVVPFNS-DSTCVIACSYEARKYGVKRGMPVREARKM 61
Query: 69 CPEIELCRVPSVRGKADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMK 128
CP + L A + YR +++ L E + +VE ASIDE ++DLT
Sbjct: 62 CPNLILV-------PARLDLYRRLSERLLSELEEVAPLVEVASIDELFLDLT-------- 106
Query: 129 SIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVYSDTDTSLMENTEDFQELAIA 188
G E+A
Sbjct: 107 ------------------GSARLLGLGS---------------------------EVA-- 119
Query: 189 GVIVEEIRAAVLSKT-QFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSMLYANLSI 247
I+ + + S GIA NK+LAKL KP +IL + + L +
Sbjct: 120 ----LRIKRHIAEQLGGITASIGIASNKLLAKLAAKYAKPDGLTILDPEDLPGFLSKLPL 175
Query: 248 KKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGIDHEPVNA 307
+ +G +E + + + +L S L + + + L+Y RGID EP++
Sbjct: 176 TDLPGIGAVTAKR-LEAVGINPIGDLLAASPDALLALWGGVSGERLWYALRGIDDEPLSP 234
Query: 308 RLVSKSIGCCKRFPGKTCLATRQDVSHWIQELADEVCERLEDDLTLNKR-RAQLLTVS-- 364
KS + P + +D ++ L +++ RL D R R L TV
Sbjct: 235 PRPRKSFSHERVLPRDSR--NAEDARPLLRLLLEKLARRLRRDGRGATRLRLWLRTVDGR 292
Query: 365 FTQETDGKVNSCSRSIALASYKLQDIVE 392
++ D S R I+ +L ++
Sbjct: 293 WSGHADIPSRSAPRPISTEDGELLHALD 320
>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 = 157 bits (400), Expect = 3e-42
Identities = 116/425 (27%), Positives = 182/425 (42%), Gaps = 102/425 (24%)
Query: 9 IDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGG----GIIA-VNYEARHKGVTRHMRGD 63
IDMD FY VE + NP L GKP+AV GG G+++ +YEAR GV M
Sbjct: 3 IDMDAFYASVEQRDNPELKGKPVAV-------GGSSDRGVVSTASYEARKFGVRSAMPIF 55
Query: 64 EAKQHCPEIELCRVPSVRGKADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVV 123
+AK+ CP + VP KYR R+++ +L + T +V
Sbjct: 56 QAKKLCPNLIF--VPP-----RFDKYREVSRQIMEILR----------------EYTPLV 92
Query: 124 HERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVYSDTDTSLMENTEDFQ 183
E + SI DE Y ++ T+ +
Sbjct: 93 -EPL-SI---------------------DE-------------AY-------LDVTDYVR 109
Query: 184 ELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSMLYA 243
A I +EIRA + +T SAGIA NK LAK+ L+KP +++P V A
Sbjct: 110 LFGSATEIAKEIRARIREETGLTASAGIAPNKFLAKIASDLNKPNGLTVIPPEDVEEFLA 169
Query: 244 NLSIKKVRHLGG----KLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARG 299
L ++K+ +G KL + ++T+ +L K ++ L+ F K+ LY +ARG
Sbjct: 170 PLPVRKIPGVGKVTAEKLKELGIKTIG-----DLAKLDVELLKKLF-GKSGRRLYELARG 223
Query: 300 IDHEPVNARLVSKSIGCCKRFPGKTCLATRQDVSHWIQELADEVCERLEDDLTLNKRRAQ 359
ID+ PV KSIG + F L +++ + ELA+E+ ERL + +
Sbjct: 224 IDNRPVEPDRERKSIGVERTFSED--LTDPEELLEELLELAEELAERLRKR----GLKGR 277
Query: 360 LLTVSFTQETDGKVNSCSRSIALASYKLQDIVEVSMQVINKTNSAPPISDLTPPLLFLGL 419
+TV D + SR++ + +DI E++++++ + PI L LG+
Sbjct: 278 TVTVKLKYA-DFSTRTRSRTLPEPTDDAEDIYELALELLEELLDGRPIR-L------LGV 329
Query: 420 SASKF 424
S
Sbjct: 330 RLSGL 334
>gnl|CDD|216135 pfam00817, IMS, impB/mucB/samB family. These proteins are involved
in UV protection.
Length = 148
Score = 144 bits (366), Expect = 5e-40
Identities = 67/213 (31%), Positives = 85/213 (39%), Gaps = 69/213 (32%)
Query: 9 IDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAKQH 68
IDMD FY VE +P L GKP+AV N G +IA +YEAR GV M EAK+
Sbjct: 1 IDMDAFYASVERLRDPELRGKPVAVGGGN--ARGVVIAASYEARKYGVKSGMPLFEAKKL 58
Query: 69 CPEIELCRVPSVRGKADISKYRNAGREVIAVLSEF-SNIVERASIDEAYIDLTDVVHERM 127
CP++ + VP D YR A R + +L F VE SIDEA++DL
Sbjct: 59 CPDLIV--VPP-----DFELYRRASRRIAEILRRFSPPKVEVYSIDEAFLDL-------- 103
Query: 128 KSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVYSDTDTSLMENTEDFQELAI 187
T L + LA
Sbjct: 104 ---------------------------------------------TGLERLFGGEEALA- 117
Query: 188 AGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKL 220
+ +R A+ +T CS GIA NK+LAKL
Sbjct: 118 -----KRLRRAIAEETGLTCSIGIAPNKLLAKL 145
>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 = 125 bits (315), Expect = 1e-30
Identities = 100/396 (25%), Positives = 152/396 (38%), Gaps = 93/396 (23%)
Query: 4 RIIALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGG----IIAVNYEARHKGVTRH 59
RII +D DCF+ V + P L GKP+AV G G I + NYEAR G+
Sbjct: 47 RIIMHVDFDCFFVSVSIRNRPDLKGKPVAVCH-----GKGPNSEIASCNYEARSYGIKNG 101
Query: 60 MRGDEAKQHCPEIELCRVPSVRGKADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDL 119
M +AK+ CP++ +P D Y +L+ +++ +E S DEA ID+
Sbjct: 102 MWVGQAKKLCPQLVT--LPY-----DFEAYEEVSLTFYEILASYTDNIEAVSCDEALIDI 154
Query: 120 TDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVYSDTDTSLMENT 179
T ++ E
Sbjct: 155 TSLLE----------------------------------------------------ETY 162
Query: 180 EDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVS 239
E +ELA E IR + T S GI N +LA+L KP Q L V
Sbjct: 163 ELPEELA------EAIRNEIRETTGCSASVGIGPNILLARLATRKAKPDGQYHLSAEKVE 216
Query: 240 MLYANLSIKKVRHLGGKLGDEVVETLQCST-MLELEKFSLKQLQSHFEEKTASWLYYIAR 298
+ L + + +G L +++V+ + LEL + ++LQ KT LY R
Sbjct: 217 EFLSQLKVGDLPGVGSSLAEKLVKLFGDTCGGLELRSKTKEKLQKVLGPKTGEKLYDYCR 276
Query: 299 GIDHEPVNARLVSKSIGC----CKRFPGKTCLATRQDVSHWIQELADEVCERLEDD-LTL 353
GID PV KS+ RF DV ++Q L++E+ +RLE+ +T
Sbjct: 277 GIDDRPVTGEKERKSVSAEINYGIRF------TNVDDVEQFLQRLSEELSKRLEESNVTG 330
Query: 354 NKRRAQLLTVSFTQETD-------GKVNSCSRSIAL 382
+ +L+ + + G +S S+S L
Sbjct: 331 RQITLKLMKRAPGAPIEPPKYMGHGICDSFSKSSTL 366
>gnl|CDD|235118 PRK03348, PRK03348, DNA polymerase IV; Provisional.
Length = 454
Score = 118 bits (298), Expect = 5e-28
Identities = 97/390 (24%), Positives = 141/390 (36%), Gaps = 109/390 (27%)
Query: 1 MTSRIIALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGG----GIIA-VNYEARHKG 55
R + +DMD F+ VE P+L G+P+ V GG G++A +YEAR G
Sbjct: 2 RAQRWVLHLDMDAFFASVEQLTRPTLRGRPVLV-------GGLGGRGVVAGASYEARVFG 54
Query: 56 VTRHMRGDEAKQHCPEIELCRVPSV----RGKADISKYRNAGREVIAVLSEFSNIVERAS 111
M +A++ L +V R YR A R V L E S +VE+ S
Sbjct: 55 ARSAMPMHQARR------LVGNGAVVLPPRFVV----YRAASRRVFDTLRELSPVVEQLS 104
Query: 112 IDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVYSDT 171
DEA+++ ++L A V +
Sbjct: 105 FDEAFVE----------------PAEL--------------AGASAEEVEAF-------- 126
Query: 172 DTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQS 231
E +RA V +T S G K +AK+ GL KP
Sbjct: 127 --------------------AERLRARVREETGLPASVGAGSGKQIAKIASGLAKPDGIR 166
Query: 232 ILPQSSVSMLYANLSIKKVRHLGG-------KLGDEVVETLQCSTMLELEKFSLKQLQSH 284
++P L A L VR L G KL +ET+ +L S ++ +
Sbjct: 167 VVPPGEERELLAPLP---VRRLWGIGPVTEEKLHRLGIETIG-----DLAALSEAEVANL 218
Query: 285 FEEKTASWLYYIARGIDHEPVNARLVSKSIGCCKRFPGKTCLATRQDVSHWIQELADEVC 344
L+ +ARGID PV R +K I F L TR + I+ +A+
Sbjct: 219 LGATVGPALHRLARGIDDRPVAERAEAKQISAESTFA--VDLTTRAQLREAIERIAEHAH 276
Query: 345 ERLEDD------LTLNKRRA--QLLTVSFT 366
RL D +T+ R++ LT S T
Sbjct: 277 RRLLKDGRGARTVTVKLRKSDFSTLTRSAT 306
>gnl|CDD|235104 PRK03103, PRK03103, DNA polymerase IV; Reviewed.
Length = 409
Score = 111 bits (280), Expect = 5e-26
Identities = 79/348 (22%), Positives = 140/348 (40%), Gaps = 75/348 (21%)
Query: 4 RIIALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGD 63
R+I L+DM FY VE NP L G+P+ V + G ++A A+ GV R
Sbjct: 3 RVILLVDMQSFYASVEKAANPELKGRPVIVSGDPERRSGVVLAACPLAKAYGVKTAERLW 62
Query: 64 EAKQHCPEIELCRVPSVRGKADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVV 123
EA+Q CP++ V K + +Y + ++ +L +F+++VE SIDE ++D+T
Sbjct: 63 EAQQKCPDL-------VVVKPRMQRYIDVSLQITRILEDFTDLVEPFSIDEQFLDVTGSQ 115
Query: 124 HERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVYSDTDTSLMENTEDFQ 183
FG
Sbjct: 116 KL--------------------FGSP---------------------------------L 122
Query: 184 ELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQS---ILPQSSVSM 240
E+A ++I+ ++ +T + GI NK+LAK+ C + L + V
Sbjct: 123 EIA------QKIQQRIMRETGVYARVGIGPNKLLAKMACDNFAKKNPDGLFTLDKEDVPA 176
Query: 241 LYANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGI 300
L ++K+ +G ++ ++ + + T+ +L L++L+ + L+ A GI
Sbjct: 177 DLWPLPVRKLFGVGSRM-EKHLRRMGIRTIGQLANTPLERLKKRW-GINGEVLWRTANGI 234
Query: 301 DHEPVNARLVS--KSIGCCKRFPGKTCLATRQDVSHWIQELADEVCER 346
D+ PV + K+IG P +++ + EL +EVC R
Sbjct: 235 DYSPVTPHSLDRQKAIGHQMTLPRD--YRGFEEIKVVLLELCEEVCRR 280
>gnl|CDD|179337 PRK01810, PRK01810, DNA polymerase IV; Validated.
Length = 407
Score = 109 bits (274), Expect = 2e-25
Identities = 48/122 (39%), Positives = 71/122 (58%), Gaps = 7/122 (5%)
Query: 3 SRIIALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRG 62
R+I +DM+ F+ VE +PSL GKPLAV + G I+ +YEAR G+ M
Sbjct: 4 GRVIFHVDMNSFFASVEIAYDPSLQGKPLAVAGNEKERKGIIVTCSYEARAYGIRTTMPL 63
Query: 63 DEAKQHCPEIELCRVPSVRGKADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDV 122
EAK+ CP++ + R P + +YR A R++ +LSEF+ +V+ SIDE Y+D+TD
Sbjct: 64 WEAKRLCPQLIV-RRP------NFDRYREASRQMFQILSEFTPLVQPVSIDEGYLDITDC 116
Query: 123 VH 124
Sbjct: 117 YA 118
Score = 51.6 bits (124), Expect = 1e-06
Identities = 44/216 (20%), Positives = 93/216 (43%), Gaps = 19/216 (8%)
Query: 191 IVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSMLYANLSIKKV 250
I + I+ +L++ Q CS GIA NK LAK+ + KP ++L + V + L + ++
Sbjct: 125 IAKMIQQRLLTELQLPCSIGIAPNKFLAKMASDMKKPLGITVLRKRDVPEMLWPLPVGEM 184
Query: 251 RHLGGKLGDEVVETLQCSTMLELEK---FSLKQLQSHFEEKTASWLYYIARGIDHEPVNA 307
+G K ++ ++ + T+ +L K L+ + A GID PV+
Sbjct: 185 HGIGEKTAEK-LKDIGIQTIGDLAKADEHILRAKLGINGVRLQRR----ANGIDDRPVDP 239
Query: 308 RLVS--KSIGCCKRFPGKTCLATRQDVSHWIQELADEVCERLEDDLTLNKRRAQLLTVSF 365
+ KS+G +++ ++ L+ V +RL+ K+ V
Sbjct: 240 EAIYQFKSVGNSTTLSHDM--DEEKELLDVLRRLSKSVSKRLQ------KKTVVSYNVQI 291
Query: 366 TQET-DGKVNSCSRSIALASYKLQDIVEVSMQVINK 400
D + + S+++ ++ +DI + + ++ +
Sbjct: 292 MIRYHDRRTITRSKTLKNPIWEKRDIFQAASRLFKQ 327
>gnl|CDD|179251 PRK01216, PRK01216, DNA polymerase IV; Validated.
Length = 351
Score = 102 bits (257), Expect = 2e-23
Identities = 84/313 (26%), Positives = 131/313 (41%), Gaps = 70/313 (22%)
Query: 5 IIALIDMDCFYCQVECKLNPSLHGKPLAVVQYN--TWKGGGIIAVNYEARHKGVTRHMRG 62
II +D D F+ QVE LNPSL GKP+ V Y+ G + NYEAR G+ M
Sbjct: 2 IILFVDFDYFFAQVEEVLNPSLKGKPVVVCVYSGRFEDSGAVATANYEARKLGIKAGMPI 61
Query: 63 DEAKQHCPEIELCRVPSVRGKADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDV 122
EAK+ P +P + ++ Y+ ++ +L E+S +E ASIDEAY+D++D
Sbjct: 62 VEAKKILPNAVY--LPM---RKEV--YQQVSNRIMKLLREYSEKIEIASIDEAYLDISDK 114
Query: 123 VHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVYSDTDTSLMENTEDF 182
V +N +D
Sbjct: 115 V-----------------------------------------------------KNYQDA 121
Query: 183 QELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSMLY 242
L EI+ +L K + + GI+ NKV AK+ + KP ++ V
Sbjct: 122 YNLG------LEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRFI 175
Query: 243 ANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGIDH 302
L I + + G + E ++ L + +++ + +L+ E A +L+ +AR +
Sbjct: 176 NELDIADIPGI-GDITAEKLKKLGVNKLVDTLRIEFDELKGIIGEAKAKYLFSLARNEYN 234
Query: 303 EPVNARLVSKSIG 315
EPV AR V KSIG
Sbjct: 235 EPVRAR-VRKSIG 246
>gnl|CDD|179473 PRK02794, PRK02794, DNA polymerase IV; Provisional.
Length = 419
Score = 96.9 bits (242), Expect = 5e-21
Identities = 86/318 (27%), Positives = 126/318 (39%), Gaps = 88/318 (27%)
Query: 6 IALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGG----IIAVNYEARHKGVTRHMR 61
IA ID D FY VE + NP L KP+ + GGG + Y AR GV M
Sbjct: 38 IAHIDCDAFYASVEKRDNPELRDKPVII-------GGGKRGVVSTACYIARIHGVRSAMP 90
Query: 62 GDEAKQHCPEIELCRVPSVRGKADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDL-- 119
+A + CP+ +V K D+ KY GREV A++ + +VE SIDEA++DL
Sbjct: 91 MFKALKLCPD-------AVVIKPDMEKYVRVGREVRAMMQALTPLVEPLSIDEAFLDLSG 143
Query: 120 TDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVYSDTDTSLMENT 179
T+ +H G A L AR A +E
Sbjct: 144 TERLH------GAPPAVVL----------------ARFARRVE----------------- 164
Query: 180 EDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVS 239
+E+ I S G+++NK LAK+ L KP+ S++ ++
Sbjct: 165 ---REIGITV------------------SVGLSYNKFLAKIASDLDKPRGFSVIGRAEAL 203
Query: 240 MLYANLSIKKVRHLGGKLGDEVVETLQ---CSTMLELEKFSLKQLQSHFEEKTASWLYYI 296
A K V + G +G L T+ +L++ L F L+ +
Sbjct: 204 AFLAP---KPVGIIWG-VGPATAARLARDGIRTIGDLQRADEADLMRRFGS-MGLRLWRL 258
Query: 297 ARGIDHEPVNARLVSKSI 314
ARGID V+ +KS+
Sbjct: 259 ARGIDDRKVSPDREAKSV 276
>gnl|CDD|235035 PRK02406, PRK02406, DNA polymerase IV; Validated.
Length = 343
Score = 91.7 bits (229), Expect = 1e-19
Identities = 43/120 (35%), Positives = 63/120 (52%), Gaps = 20/120 (16%)
Query: 11 MDCFYCQVECKLNPSLHGKPLAVVQYNTWKGG-----GIIAV-NYEARHKGVTRHMRGDE 64
MDCFY VE + NP L GKP+AV GG G+I+ NYEAR GV M +
Sbjct: 1 MDCFYAAVEMRDNPELRGKPVAV-------GGSPGRRGVISTCNYEARKFGVRSAMPTAQ 53
Query: 65 AKQHCPEIELCRVPSVRGKADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVH 124
A + CP++ VP Y+ R++ + +++++E S+DEAY+D+TD
Sbjct: 54 ALKLCPDLIF--VPG-----RFDVYKEVSRQIREIFRRYTDLIEPLSLDEAYLDVTDNKL 106
Score = 87.5 bits (218), Expect = 2e-18
Identities = 54/177 (30%), Positives = 83/177 (46%), Gaps = 18/177 (10%)
Query: 179 TEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQS-ILPQSS 237
T++ + A +I +EIR + + SAG+A NK LAK+ +KP I P+
Sbjct: 102 TDNKLCIGSATLIAQEIRQDIFEELGLTASAGVAPNKFLAKIASDWNKPNGLFVITPEEV 161
Query: 238 VSMLYANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIA 297
+ L A L ++K+ GK+ E + L T +L+K+ L +L HF K LY A
Sbjct: 162 DAFL-ATLPVEKI-PGVGKVTAEKLHALGIYTCADLQKYDLAELIRHF-GKFGRRLYERA 218
Query: 298 RGIDHEPVNARLVSKSIGCCKRFPGKTCLATRQDVSHW------IQELADEVCERLE 348
RGID PV KS+G + A +D+ + LA+++ RLE
Sbjct: 219 RGIDERPVKPDRERKSVG------VERTFA--EDLYDLEACLAELPRLAEKLERRLE 267
>gnl|CDD|179663 PRK03858, PRK03858, DNA polymerase IV; Validated.
Length = 396
Score = 89.7 bits (223), Expect = 7e-19
Identities = 39/112 (34%), Positives = 63/112 (56%), Gaps = 15/112 (13%)
Query: 10 DMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGII-AVNYEARHKGVTRHMRGDEAKQH 68
D+D FY VE + +P+L G+P+ V GGG++ A +YEA+ GV M G +A++
Sbjct: 10 DLDSFYASVEQRDDPALRGRPVIV-------GGGVVLAASYEAKAYGVRTAMGGRQARRL 62
Query: 69 CPEIELCRVPSVRGKADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLT 120
CP+ + V + +S Y A + V V + + +VE SIDEA++D+
Sbjct: 63 CPQAVV-----VPPR--MSAYSRASKAVFEVFRDTTPLVEGLSIDEAFLDVG 107
>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 = 89.1 bits (221), Expect = 1e-18
Identities = 47/137 (34%), Positives = 75/137 (54%), Gaps = 19/137 (13%)
Query: 10 DMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAKQHC 69
D+DCFY QVE +PSL KPL + Q ++ NYEAR GV + M +AK+ C
Sbjct: 4 DLDCFYAQVEEIRDPSLKSKPLGIQQKYI-----VVTCNYEARRLGVKKLMSIKDAKEIC 58
Query: 70 PEIELCRVPSVRGKADISKYRNAGREVIAVLSEFS--NIVERASIDEAYIDLTDVVHERM 127
P++ L V G+ D++ +R+ ++V +L +S + VER DE ++D+T++ R+
Sbjct: 59 PDLVL-----VNGE-DLTPFRDMSKKVYRLLRSYSWNDRVERLGFDENFMDVTEM---RL 109
Query: 128 KSIGHIAA---SQLSNT 141
HIA ++ N
Sbjct: 110 LVASHIAYEMRERIENE 126
Score = 66.0 bits (161), Expect = 3e-11
Identities = 58/255 (22%), Positives = 102/255 (40%), Gaps = 31/255 (12%)
Query: 185 LAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSIL--PQSSVSMLY 242
L +A I E+R + ++ C AGIA NK+LAKLV ++KP +Q+ L P + M +
Sbjct: 109 LLVASHIAYEMRERIENELGLTCCAGIASNKLLAKLVGSVNKPNQQTTLLPPSCADLMDF 168
Query: 243 ANL-SIKKVRHLGGKLGDEVVETL--------QCSTMLELEK------FSLKQLQSHFEE 287
+L ++K+ +G K ++ + S L + F E
Sbjct: 169 MDLHDLRKIPGIGYKTAAKLEAHGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEFGE 228
Query: 288 KTASWLYYIARGIDHEPVN-ARLVSKSIGCCKRFPGKTCLATRQDVSHWIQELADEVCER 346
++ + G D PV A + I + K L ++ + I+EL + ER
Sbjct: 229 GIGQRIWKLLFGRDTSPVKPASDFPQQISIEDSYK-KCSLEEIREARNKIEELLASLLER 287
Query: 347 LEDDLTLNK----RRAQLLTVSFTQETDGKVNS--CSRSIALASYKLQDIVEVSMQVINK 400
++ DL K RR L ++ + T K + S+ + S+ + +
Sbjct: 288 MKQDLQEVKAGDGRRPHTLRLTLRRYTSTKKHYNRESKQAPIPSH----VFQKLTG--GN 341
Query: 401 TNSAPPISDLTPPLL 415
+A PI + L
Sbjct: 342 EIAARPIEKILMRLF 356
>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 = 76.4 bits (189), Expect = 1e-14
Identities = 35/117 (29%), Positives = 53/117 (45%), Gaps = 12/117 (10%)
Query: 7 ALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAK 66
AL+D + FY E P L G+PL V+ N G +IA + EA+ G+ +
Sbjct: 1 ALVDCNSFYASCERVFRPLLLGRPLVVLSNN---DGCVIARSPEAKALGIKMGSPYFKVP 57
Query: 67 QHCPEIELCRVPSVRGK--ADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTD 121
+ S D+S R ++++L FS VE SIDE+++DLT
Sbjct: 58 DLLERHGVAVFSS-NYALYGDMS------RRIMSILERFSPDVEVYSIDESFLDLTG 107
Score = 59.1 bits (144), Expect = 5e-09
Identities = 41/188 (21%), Positives = 63/188 (33%), Gaps = 38/188 (20%)
Query: 191 IVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHK--PQKQSILPQSSVSMLYANLSIK 248
+ +IR +L +T + GI K LAKL L K ++ + + L I
Sbjct: 117 LARKIRRRILQETGIPVTVGIGPTKTLAKLANDLAKKKNPYGGVVDLTDEEVRDKLLKIL 176
Query: 249 KV-------RHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGID 301
V R KL + T +L + L+ F L GID
Sbjct: 177 PVGDVWGIGRRTAKKL-----NAMGIHTAGDLAQADPDLLRKKF-GVVGERLVRELNGID 230
Query: 302 HEPV-NARLVSKSIGCCKRFPGKTCLATRQDVSHW------IQELADEVCERLEDDLTLN 354
P+ KSIG + F +DV+ + E A+ E+L
Sbjct: 231 CLPLEEYPPPKKSIGSSRSFG--------RDVTDLDELKQALAEYAERAAEKL------- 275
Query: 355 KRRAQLLT 362
RR + +
Sbjct: 276 -RRQKSVA 282
>gnl|CDD|184529 PRK14133, PRK14133, DNA polymerase IV; Provisional.
Length = 347
Score = 75.1 bits (185), Expect = 3e-14
Identities = 47/127 (37%), Positives = 67/127 (52%), Gaps = 21/127 (16%)
Query: 2 TSRIIALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGG----GIIAV-NYEARHKGV 56
R+I +DMD F+ VE NP L GKP+ V GG G+++ +YEAR GV
Sbjct: 1 MDRVIIHVDMDAFFASVEQMDNPKLKGKPVIV-------GGISERGVVSTCSYEARKYGV 53
Query: 57 TRHMRGDEAKQHCPE-IELCRVPSVRGKADISKYRNAGREVIAVLSEFSNIVERASIDEA 115
M AK+ CP I L VR + +Y+ + + +L E + IVE SIDEA
Sbjct: 54 HSAMPVFMAKKRCPHGIFL----PVRHE----RYKEVSKNIFKILYEVTPIVEPVSIDEA 105
Query: 116 YIDLTDV 122
Y+D+T++
Sbjct: 106 YLDITNI 112
Score = 56.3 bits (136), Expect = 4e-08
Identities = 59/237 (24%), Positives = 107/237 (45%), Gaps = 18/237 (7%)
Query: 191 IVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSMLYANLSIKKV 250
I + I+ V +T S GI++NK LAKL +KP I+ + + + L I KV
Sbjct: 119 IAKYIKKKVKKETGLTLSVGISYNKFLAKLASDWNKPDGIKIITEDMIPDILKPLPISKV 178
Query: 251 RHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGIDHEPVNARLV 310
+G K E + + T+ +L K S + L +F K +Y RGID+ V
Sbjct: 179 HGIGKKSV-EKLNNIGIYTIEDLLKLSREFLIEYF-GKFGVEIYERIRGIDYREVEVSRE 236
Query: 311 SKSIGCCKRFPGKTCLATRQDVSHWIQELADEVCERLEDDLTLNKRRAQLLTVSFTQET- 369
KSIG K K ++++ ++++ ++ + E L KR TV+ +T
Sbjct: 237 RKSIG--KETTLKKDTKDKEELKKYLKDFSNIISE------ELKKRNLYGKTVTVKIKTS 288
Query: 370 DGKVNSCSRSIALASYKLQDIVEVSMQVINKTNSAPPISDLTPPLLFLGLSASKFSP 426
D + ++ S+++ ++I V+ +++ ++ P+ +GLS S S
Sbjct: 289 DFQTHTKSKTLNDYIRDKEEIYNVACEILEH-------INIKEPIRLIGLSVSNLSE 338
>gnl|CDD|221229 pfam11799, IMS_C, impB/mucB/samB family C-terminal. These proteins
are involved in UV protection.
Length = 136
Score = 69.1 bits (169), Expect = 7e-14
Identities = 30/87 (34%), Positives = 42/87 (48%), Gaps = 6/87 (6%)
Query: 279 KQLQSHFEEKTASWLYYIARGIDHEPVNARLVSKSIGCCKRFPGKTCLATRQDVSHWIQE 338
+LQ F T LY +ARGID +PV R KSI + FP L R+++ +
Sbjct: 1 AELQKRFGGVTGERLYNLARGIDDDPVEPREERKSISSERTFPRD--LTDREELEALLLR 58
Query: 339 LADEVCERLEDDLTLNKRRAQLLTVSF 365
LA+E+ ERL A+ +TV
Sbjct: 59 LAEELAERLRR----RGLAARTVTVKL 81
>gnl|CDD|179564 PRK03352, PRK03352, DNA polymerase IV; Validated.
Length = 346
Score = 73.9 bits (182), Expect = 8e-14
Identities = 81/360 (22%), Positives = 123/360 (34%), Gaps = 91/360 (25%)
Query: 1 MTSRIIALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGG--------GIIA-VNYEA 51
R + +D+D F VE P L G P+ V GG ++ +YEA
Sbjct: 2 AMPRWVLHVDLDQFIAAVELLRRPELAGLPVIV-------GGNGDPTEPRKVVTCASYEA 54
Query: 52 RHKGVTRHMRGDEAKQHCPEIELCRVPSVRGKADISKYRNAGREVIAVLSEFSNIVERAS 111
R GV M A + CP+ +PS D + Y A EV+A L + VE
Sbjct: 55 RAFGVRAGMPLRTAARRCPDAVF--LPS-----DPAAYDAASEEVMATLRDLGVPVEVWG 107
Query: 112 IDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVYSDT 171
DEA+ +G D+ + A
Sbjct: 108 WDEAF---------------------------LGVDTDDPEALAE--------------- 125
Query: 172 DTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQS 231
I ++E T CS GI NK+ AK+ G KP
Sbjct: 126 --------------EIRAAVLER--------TGLSCSVGIGDNKLRAKIATGFAKPAGVF 163
Query: 232 ILPQSSVSMLYANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTAS 291
L ++ + + + +G K + L +T+ +L +L + F T
Sbjct: 164 RLTDANWMAVMGDRPTDALWGVGPKTAKRLAA-LGITTVADLAAADPAELAATFGPTTGP 222
Query: 292 WLYYIARGIDHEPVNAR-LVSKSIGCCKRFPGKTCLATRQDVSHWIQELADEVCERLEDD 350
WL +ARG V+A V +S FP L R +V ++ELA V + + +
Sbjct: 223 WLLLLARGGGDTEVSAEPWVPRSRSREVTFPQD--LTDRAEVESAVRELARRVLDEVVAE 280
>gnl|CDD|179607 PRK03609, umuC, DNA polymerase V subunit UmuC; Reviewed.
Length = 422
Score = 53.2 bits (128), Expect = 4e-07
Identities = 48/147 (32%), Positives = 67/147 (45%), Gaps = 13/147 (8%)
Query: 7 ALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAK 66
AL D++ FY E P L GKP+ V+ N G +IA + EA+ G+ M K
Sbjct: 3 ALCDVNSFYASCETVFRPDLRGKPVVVLSNND---GCVIARSAEAKALGIK--MGDPWFK 57
Query: 67 QHCPEIELCRVPSVRGKADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHER 126
Q + R V ++ Y + V++ L E S VE SIDEA+ DLT V + R
Sbjct: 58 Q---KDLFRRCGVVCFSSNYELYADMSNRVMSTLEELSPRVEIYSIDEAFCDLTGVRNCR 114
Query: 127 -MKSIGH-IAASQLSNTFV---VGFGP 148
+ G I A+ L T + VG
Sbjct: 115 DLTDFGREIRATVLQRTHLTVGVGIAQ 141
Score = 30.1 bits (68), Expect = 6.1
Identities = 15/27 (55%), Positives = 16/27 (59%)
Query: 194 EIRAAVLSKTQFHCSAGIAHNKVLAKL 220
EIRA VL +T GIA K LAKL
Sbjct: 122 EIRATVLQRTHLTVGVGIAQTKTLAKL 148
>gnl|CDD|176458 cd03468, PolY_like, DNA Polymerase Y-family. 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. 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 = 335
Score = 42.8 bits (101), Expect = 8e-04
Identities = 38/182 (20%), Positives = 59/182 (32%), Gaps = 21/182 (11%)
Query: 198 AVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSMLYANLSIKKVRHLGGK- 256
A L+ AGIA A L+ + +L + + L A L + +
Sbjct: 123 AALATLGLSARAGIADTPGAAWLLARAGGGRG--VLRREA---LAAALVLLAPLPVAALR 177
Query: 257 LGDEVVETLQ---CSTMLELEKFSLKQLQSHFEEKTASWLYYIARGIDHEPVNARLVSKS 313
L E VE L T+ +L +L F A G D EP+
Sbjct: 178 LPPETVELLARLGLRTLGDLAALPRAELARRF-GLALLLRLDQAYGRDPEPLLFSP---- 232
Query: 314 IGCCKRFPGKTCLATRQDVSHWIQEL--ADEVCERLEDDLTLNKRRAQLLTVSFTQETDG 371
F L + + L + E+L L L A+ L+++ DG
Sbjct: 233 --PPPAFD--FRLELQLEEPIARGLLFPLRRLLEQLCAFLALRGLGARRLSLTL-FREDG 287
Query: 372 KV 373
+V
Sbjct: 288 RV 289
>gnl|CDD|236304 PRK08581, PRK08581, N-acetylmuramoyl-L-alanine amidase; Validated.
Length = 619
Score = 37.5 bits (87), Expect = 0.041
Identities = 50/304 (16%), Positives = 92/304 (30%), Gaps = 27/304 (8%)
Query: 577 DVLFNEKVENLTMENKKSIKNECLSPVSSKSKDLTNENLGHTFETLPSPILTSDRDIHTS 636
D + + + ++KKS +E SSK D + N + T D S
Sbjct: 29 DPQKDSTAKTTSHDSKKSNDDETSKDTSSKDTDKADNNNTSNQDNNDKKFSTIDSSTSDS 88
Query: 637 TPCRRKGSKNVFENKTLKSKEELPLVKRVDN-----TIPNSFEFITYTRRQVKPENISNG 691
KN+ + + L K DN I N F + +P N
Sbjct: 89 NNIIDFIYKNLPQTNI---NQLLTKNKYDDNYSLTTLIQNLFNLNSDISDYEQPRNSEKS 145
Query: 692 NNSDNKTDDEDSPQVITKPIGSISMRKYETTRQSHLN-----KPKLFADFPTTSQGNNP- 745
N NK D K K + KP P + + P
Sbjct: 146 TNDSNKNSDSS-----IKNDTDTQSSKQDKADNQKAPSSNNTKPSTSNKQPNSPKPTQPN 200
Query: 746 DTHEPPNSSNKRGKSYSFFENYLRRKKERERLNSKSCKDETLTHGQVHPSVETNTHTILE 805
++ P S + + S +N + + + +D T + +
Sbjct: 201 QSNSQPASDDTANQKSSSKDNQSMSDSALDSILDQYSEDAKKTQKDYASQSKKDKTETSN 260
Query: 806 EVTSSIETVDNGSIETNAMTRIRDDIHLARENNTK----FLADP-IKDTESTGPSNVIST 860
+ T D ++ +D+ ++NT+ F P + + + +G NV+ +
Sbjct: 261 TKNPQLPTQDELKHKSKPAQSFENDV---NQSNTRSTSLFETGPSLSNNDDSGSFNVVDS 317
Query: 861 ESNE 864
+
Sbjct: 318 KDTR 321
>gnl|CDD|140232 PTZ00205, PTZ00205, DNA polymerase kappa; Provisional.
Length = 571
Score = 36.2 bits (83), Expect = 0.098
Identities = 22/64 (34%), Positives = 31/64 (48%), Gaps = 5/64 (7%)
Query: 9 IDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAKQH 68
+DMD FY VE K +P PLA+ + NY AR +G+ + M G A +
Sbjct: 138 LDMDMFYAAVEIKKHPEYAAIPLAIGTMTM-----LQTANYVARGRGIRQGMPGFLALKI 192
Query: 69 CPEI 72
CP +
Sbjct: 193 CPNL 196
Score = 35.0 bits (80), Expect = 0.26
Identities = 43/216 (19%), Positives = 83/216 (38%), Gaps = 30/216 (13%)
Query: 180 EDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSIL---PQS 236
E F+ A + E+R V +T+ SAGI LAK+ ++KP Q L +
Sbjct: 241 ERFEGTKTAEDVASELRVRVFGETKLTASAGIGPTAALAKIASNINKPNGQHDLNLHTRG 300
Query: 237 SVSMLYANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYI 296
V +L ++ V + GK+ + +++ L +T+ ++ + +L +L
Sbjct: 301 DVMTYVRDLGLRSVPGV-GKVTEALLKGLGITTLSDIYNRRV-ELCYILHNNLFRFLLGA 358
Query: 297 ARGIDHEPVNARLVS------------KSIGCCKRFPGKTCLATRQDVSHWIQELADE-- 342
+ GI P A + K+I + F T T++ + + + +
Sbjct: 359 SIGIMQWPDAATAANTENCEGATGGQRKAISSERSF---TTPRTKEGLQEMVDTVFNGAY 415
Query: 343 --------VCERLEDDLTLNKRRAQLLTVSFTQETD 370
+C ++ + R Q T S Q +D
Sbjct: 416 EEMRKSELMCRQISLTIRWASYRYQQYTKSLIQYSD 451
>gnl|CDD|219444 pfam07516, SecA_SW, SecA Wing and Scaffold domain. SecA protein
binds to the plasma membrane where it interacts with
proOmpA to support translocation of proOmpA through the
membrane. SecA protein achieves this translocation, in
association with SecY protein, in an ATP dependent
manner. This family is composed of two C-terminal alpha
helical subdomains: the wing and scaffold subdomains.
Length = 213
Score = 35.2 bits (82), Expect = 0.10
Identities = 27/142 (19%), Positives = 52/142 (36%), Gaps = 37/142 (26%)
Query: 467 KTLLNF----NQQTPFQLALNRIERKLIDKFKSHIESKLDSCNANVDKLVIGDISEQIKN 522
K LL + N+Q RK+I ++ I L D+ E I
Sbjct: 27 KNLLEYDDVMNEQ-----------RKVIYAQRNEI-------------LEGEDLKEIILE 62
Query: 523 IAAENVRKYLRTH-SKDSNASDEDEESFNDKL-------VSIEREVEESVGK-DIEESLK 573
+ + + + + + S + D E ++L + I+ E E + + +++E L
Sbjct: 63 MIEDVIDDIVEEYAPEKSYPEEWDLEGLEEELRELLGLDLDIDEEELEGLTEEELKERLI 122
Query: 574 NVSDVLFNEKVENLTMENKKSI 595
+ + EK L E + I
Sbjct: 123 EAAKEAYEEKEAELGEELMREI 144
>gnl|CDD|227578 COG5253, MSS4, Phosphatidylinositol-4-phosphate 5-kinase [Signal
transduction mechanisms].
Length = 612
Score = 33.4 bits (76), Expect = 0.76
Identities = 23/146 (15%), Positives = 45/146 (30%), Gaps = 11/146 (7%)
Query: 743 NNPDTHEPPNSSNKRGKSYSFFENYLRRKKERERLNSKSCKDETLTHGQVHPSVETNTHT 802
N N SN K+ S R L+ + + Q +
Sbjct: 114 PNHTRSSGNNLSNANVKTLSAPVGEHSRSNNPPNLDQNLDTEPESSISQWGELQLNPSGK 173
Query: 803 ILEEVTSSIETVDNGSIETN------AMTRIRDDIHLARENNTKFLADP-----IKDTES 851
L S T +N E++ ++ D L + + F A+
Sbjct: 174 TLSSQPSRKPTSENPKSESDNSKLPTSVNSPLPDKSLLKRTLSNFWAERNSYNWKPLVYP 233
Query: 852 TGPSNVISTESNEVIDQTKIRDVSSS 877
+ PS I ++S+ +I + + + +
Sbjct: 234 SCPSEHIFSDSDVIIREDEPSSLIAF 259
>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen;
Provisional.
Length = 1136
Score = 32.1 bits (72), Expect = 1.9
Identities = 35/159 (22%), Positives = 69/159 (43%), Gaps = 11/159 (6%)
Query: 463 KKRDKTLLNFNQQTPFQLALNRIERKLIDK-FKSHIESKLDSCNANVDKLVIGDISEQIK 521
K+DK + + + I LI+K K+ E+ + + + + D E ++
Sbjct: 899 GKKDKKAKKKDAKDLSGNIAHEI--NLINKELKNQNENVPEHLKEHAEANIEEDAEENVE 956
Query: 522 NIAAENVRKYLRTHSKDSNASDEDEESFNDKLVSIEREVEESVGKDIEESLKNVSDVLFN 581
A ENV + + + N + EE+ + ++E VEE+V +++EE+++ +
Sbjct: 957 EDAEENVEENV-----EENVEENVEENVEE---NVEENVEENVEENVEENVEENIEENVE 1008
Query: 582 EKVENLTMENKKSIKNECLSPVSSKSKDLTNENLGHTFE 620
E VE EN + E + V ++ EN+ E
Sbjct: 1009 ENVEENIEENVEEYDEENVEEVEENVEEYDEENVEEIEE 1047
>gnl|CDD|237259 PRK12904, PRK12904, preprotein translocase subunit SecA; Reviewed.
Length = 830
Score = 31.6 bits (73), Expect = 2.5
Identities = 19/86 (22%), Positives = 37/86 (43%), Gaps = 9/86 (10%)
Query: 515 DISEQIKNIAAENVRKYLRTH-SKDSNASDEDEESFNDKL-------VSIEREVEESVGK 566
D+SE I ++ + + + + S D D E + L + IE +EE + +
Sbjct: 653 DLSETILDMREDVIEDLVDAYIPPGSYEEDWDLEGLEEALKTDFGLELPIEEWLEEGLDE 712
Query: 567 D-IEESLKNVSDVLFNEKVENLTMEN 591
+ + E + ++ + EK E L E
Sbjct: 713 EELRERILEAAEEAYEEKEEELGEEQ 738
>gnl|CDD|218791 pfam05879, RHD3, Root hair defective 3 GTP-binding protein (RHD3).
This family consists of several eukaryotic root hair
defective 3 like GTP-binding proteins. It has been
speculated that the RHD3 protein is a member of a novel
class of GTP-binding proteins that is widespread in
eukaryotes and required for regulated cell enlargement.
The family also contains the homologous yeast synthetic
enhancement of YOP1 (SEY1) protein which is involved in
membrane trafficking.
Length = 743
Score = 31.3 bits (71), Expect = 3.3
Identities = 18/62 (29%), Positives = 24/62 (38%), Gaps = 2/62 (3%)
Query: 320 FPGKTCLATRQDVSHWIQELADEVCERLEDDLT-LNKRRAQLLTVSFTQETDGKVNSCSR 378
PG A + V I L E + T L + + + L V F +E D V R
Sbjct: 582 EPGTVNPADEESV-TSIDGLDSSEWEEVPSFATILTEVQKKSLWVQFKKEADYTVTEAKR 640
Query: 379 SI 380
SI
Sbjct: 641 SI 642
>gnl|CDD|178321 PLN02719, PLN02719, triacylglycerol lipase.
Length = 518
Score = 30.8 bits (69), Expect = 4.0
Identities = 29/98 (29%), Positives = 39/98 (39%), Gaps = 17/98 (17%)
Query: 251 RHLGGKLG-----DEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGIDHEPV 305
RHL LG EV L ++ + L F K S K A+W+ Y+A D E
Sbjct: 147 RHLFDSLGIIDSGYEVARYLYATSNINLPNFFSKSRWSKVWSKNANWIGYVAVSDDDEAT 206
Query: 306 NARLVSKSIGCCKRFPGKTCLATRQDVS--HWIQELAD 341
RL + I +A R V+ WI +L D
Sbjct: 207 RCRLGRRDIA----------IAWRGTVTRLEWIADLKD 234
>gnl|CDD|222080 pfam13369, Transglut_core2, Transglutaminase-like superfamily.
Length = 154
Score = 29.6 bits (67), Expect = 4.7
Identities = 8/38 (21%), Positives = 16/38 (42%)
Query: 330 QDVSHWIQELADEVCERLEDDLTLNKRRAQLLTVSFTQ 367
+ V + LA EV RL + ++ L + + +
Sbjct: 1 EQVLAQLDALAAEVRARLPAEADPLEKLEALNRLLYGE 38
>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 = 30.2 bits (68), Expect = 5.2
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 2/73 (2%)
Query: 92 AGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNN 151
A E I VL+ + ++ A ID Y+ + M++ +AA+ N F++G P +N
Sbjct: 75 AKDEGIKVLA-YDRLINDADID-FYLSFDNEKVGEMQAKAVLAAAPKGNYFLMGGSPTDN 132
Query: 152 DEDARKAGVMEWL 164
+ + G M+ L
Sbjct: 133 NAKLLRGGQMKVL 145
>gnl|CDD|197483 smart00038, COLFI, Fibrillar collagens C-terminal domain. Found at
C-termini of fibrillar collagens: Ephydatia muelleri
procollagen EMF1alpha, vertebrate collagens alpha(1)III,
alpha(1)II, alpha(2)V etc.
Length = 232
Score = 29.7 bits (67), Expect = 6.5
Identities = 15/67 (22%), Positives = 31/67 (46%), Gaps = 5/67 (7%)
Query: 816 NGSIETNAMTRIRDDIHLARENNTKFLADPIKDTESTGPSN----VISTESNEVIDQTKI 871
G+++ R +D+ L+ E N+KF + ++D VI + + ++ I
Sbjct: 149 TGNLKKALRLRGSNDVELSAEGNSKFTYEVLEDGCQKRTGKWGKTVIEYRTKKT-ERLPI 207
Query: 872 RDVSSSD 878
D++ SD
Sbjct: 208 VDIAPSD 214
>gnl|CDD|221952 pfam13166, AAA_13, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. This family includes the
PrrC protein that is thought to be the active component
of the anticodon nuclease.
Length = 713
Score = 29.6 bits (67), Expect = 9.8
Identities = 24/125 (19%), Positives = 51/125 (40%), Gaps = 10/125 (8%)
Query: 490 IDKFKSHIESKLDSCNANVDKLVIGDISEQIKN-IAAENVRKYLRTHSKDSNASDEDEES 548
++K +E KL + +++ I D+ E I + I A N +R H++ + +++
Sbjct: 336 LEKNLQKLEEKLKDPSTSIELESITDLIESINDIIDAINE--LIREHNEKIDNLKKEKNK 393
Query: 549 FNDKLVSIEREVEESVGKDIEESLKNVSDVLFNEKVENLTMENKKSIKNECLSPVSSKSK 608
KL + DI+ K + EK N ++E + + + + K
Sbjct: 394 AKKKLWLHLVAELKE---DIDAYQKEKKGL---EKAIN-SLEKEIKQLEAEIKALEKEIK 446
Query: 609 DLTNE 613
+L +
Sbjct: 447 ELEKQ 451
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
0.311 0.127 0.357
Gapped
Lambda K H
0.267 0.0653 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 50,338,851
Number of extensions: 4847290
Number of successful extensions: 3584
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3494
Number of HSP's successfully gapped: 82
Length of query: 1041
Length of database: 10,937,602
Length adjustment: 107
Effective length of query: 934
Effective length of database: 6,191,724
Effective search space: 5783070216
Effective search space used: 5783070216
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: 64 (28.6 bits)