Query psy5919
Match_columns 387
No_of_seqs 329 out of 861
Neff 6.8
Searched_HMMs 46136
Date Fri Aug 16 21:48:37 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5919.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5919hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00166 DNA polymerase delta 100.0 9.8E-36 2.1E-40 330.4 21.9 163 93-258 80-250 (1054)
2 KOG0969|consensus 100.0 9.5E-35 2.1E-39 299.6 10.8 180 2-258 75-260 (1066)
3 PF13901 DUF4206: Domain of un 99.9 1.9E-27 4.1E-32 219.9 1.7 133 242-387 10-150 (202)
4 KOG0968|consensus 99.9 4.6E-25 1E-29 234.9 4.6 202 35-287 49-270 (1488)
5 KOG1829|consensus 99.9 4.1E-23 8.8E-28 213.3 4.4 133 242-387 368-509 (580)
6 PF03104 DNA_pol_B_exo1: DNA p 99.8 1.3E-20 2.8E-25 184.5 5.9 145 95-258 1-146 (325)
7 PRK05761 DNA polymerase I; Rev 99.5 1.1E-13 2.3E-18 151.1 10.5 124 84-233 29-153 (787)
8 PRK05762 DNA polymerase II; Re 99.3 3E-12 6.5E-17 140.3 10.4 115 84-228 16-130 (786)
9 COG0417 PolB DNA polymerase el 98.9 7.3E-09 1.6E-13 113.8 11.2 129 85-230 6-134 (792)
10 KOG0969|consensus 98.8 3.1E-09 6.7E-14 111.9 4.8 39 81-119 90-128 (1066)
11 PTZ00166 DNA polymerase delta 97.8 2.2E-05 4.7E-10 89.0 5.5 62 2-70 42-109 (1054)
12 PF13901 DUF4206: Domain of un 97.4 0.00017 3.7E-09 67.0 4.2 58 290-347 100-157 (202)
13 KOG1798|consensus 97.2 0.00094 2E-08 75.5 8.1 127 87-228 69-226 (2173)
14 TIGR00592 pol2 DNA polymerase 97.0 0.0064 1.4E-07 70.1 13.3 160 86-256 321-493 (1172)
15 PF03104 DNA_pol_B_exo1: DNA p 96.1 0.0027 5.8E-08 62.1 1.9 27 44-70 2-28 (325)
16 PRK05762 DNA polymerase II; Re 96.0 0.0085 1.8E-07 66.5 5.3 49 2-68 4-52 (786)
17 KOG0968|consensus 95.1 0.0095 2.1E-07 66.3 1.8 59 85-143 47-106 (1488)
18 KOG0970|consensus 93.7 0.22 4.9E-06 55.9 8.1 152 88-258 349-517 (1429)
19 KOG1829|consensus 85.2 0.49 1.1E-05 50.4 2.0 57 292-348 461-517 (580)
20 COG0417 PolB DNA polymerase el 79.2 2.1 4.6E-05 47.7 4.3 36 33-68 6-41 (792)
21 TIGR00592 pol2 DNA polymerase 66.6 1.9 4.2E-05 50.1 0.1 53 169-224 128-180 (1172)
22 cd05767 IgC_MHC_II_alpha Class 63.1 8.5 0.00018 31.1 3.2 24 36-59 2-29 (94)
23 cd05767 IgC_MHC_II_alpha Class 49.8 22 0.00047 28.7 3.5 24 88-111 2-29 (94)
24 cd05770 IgC_beta2m Class I maj 46.1 24 0.00053 28.4 3.3 25 36-60 2-30 (93)
25 cd05766 IgC_MHC_II_beta Class 38.7 37 0.0008 27.2 3.3 24 36-59 1-28 (94)
26 cd05770 IgC_beta2m Class I maj 34.8 54 0.0012 26.4 3.6 25 88-112 2-30 (93)
27 PRK05761 DNA polymerase I; Rev 34.1 36 0.00078 38.1 3.3 37 32-69 29-66 (787)
28 TIGR00778 ahpD_dom alkylhydrop 31.7 21 0.00046 24.7 0.7 25 362-386 1-25 (50)
29 cd07698 IgC_MHC_I_alpha3 Class 29.8 61 0.0013 25.5 3.2 25 36-60 3-29 (93)
30 cd07698 IgC_MHC_I_alpha3 Class 21.4 1.2E+02 0.0026 23.8 3.4 26 87-112 2-29 (93)
31 cd05772 IgC_SIRP Signal-regula 21.0 81 0.0017 26.2 2.4 27 33-59 6-35 (111)
No 1
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=100.00 E-value=9.8e-36 Score=330.36 Aligned_cols=163 Identities=33% Similarity=0.526 Sum_probs=122.5
Q ss_pred EEecCCCCEEEEEEceeeeEEEEecCCCCchHHHHHHHHHHHHHHHHHHcCCCCCcceEEEEEEEEeeceecccC-CceE
Q psy5919 93 FGNNVEGKKTCVFVHGVFPYLYIPFHHEPITETMLQQLAASIDKALNIALGYKDSVQHVFHISICKKFPMYGYHA-DERT 171 (387)
Q Consensus 93 FG~T~~G~svcv~Vhgf~PYfYv~~~~~~~~~~~l~~l~~~l~~~l~~s~~~~~~~~~V~~ie~V~~~~~YGY~~-~~~~ 171 (387)
||+|++|+|||||||||+|||||++|+++..+ ++..+...|++.+..+.........|.+|++|+|++||||++ ++.+
T Consensus 80 FGvTe~G~SV~v~V~gF~PYFYV~~p~~~~~~-~~~~~~~~L~~~l~~~~~~~~~~~~V~~VeiV~k~sl~gY~~~~~~~ 158 (1054)
T PTZ00166 80 YGVTKEGHSVLVNVHNFFPYFYIEAPPNFLPE-DSQKLKRELNAQLSEQSQFKKYQNTVLDIEIVKKESLMYYKGNGEKD 158 (1054)
T ss_pred EEecCCCCEEEEEEeCCceEEEEecCCCCCHH-HHHHHHHHHHHHHhhcccccccCCceEEEEEEEeeeeceeCCCCcee
Confidence 44445555555555555555555555544332 455666666655443210001346899999999999999997 5789
Q ss_pred EEEEEecCcchHHHHHHHHhCCcccC-------CccceeccCcchhhhhhhhcCCcceeeEEecceeEEecCCCCCCCCC
Q psy5919 172 FLKILLYEPYHMSKLEDLLLNGAVFN-------ERFQPYESHIPYILQFCIDYNLYGMSNIEFNMVKFRSDSETSLPKLS 244 (387)
Q Consensus 172 FlKI~~~~P~~v~~l~~lL~~g~~~~-------~~~q~yEahIp~~lrFmiD~nL~G~~wi~~~~~~~r~~~~~~~~r~S 244 (387)
|+||++.+|.+++++|++|++|..++ ..+++|||||||++|||+|+||.||+||+++++++.....+ .+.|
T Consensus 159 flKIt~~~P~~v~klR~~Le~g~~~~~~~~~~~~~~~vyEsnI~f~lRFmID~~I~g~~Wi~i~~~~~~~~~~~--~~~s 236 (1054)
T PTZ00166 159 FLKITVQLPKMVPRLRSLIESGVVVCGGGWDGIRLFQTYESNVPFVLRFLIDNNITGGSWLTLPKGKYKIRPPK--KKTS 236 (1054)
T ss_pred EEEEEEcCHHHHHHHHHHHHcCCcccccccccccccceeecCCCHHHHHHhccCCCceeEEEecCcceeecccc--cCCC
Confidence 99999999999999999999986432 34799999999999999999999999999999888655432 5789
Q ss_pred ccceeeEeecccce
Q psy5919 245 HCQLEADVKAESIV 258 (387)
Q Consensus 245 ~C~lEiDv~~~~Il 258 (387)
+|++|++|.+.+|.
T Consensus 237 ~c~~E~~~~~~~l~ 250 (1054)
T PTZ00166 237 TCQIEVDCSYEDLI 250 (1054)
T ss_pred cceEEEEEehhhee
Confidence 99999999998876
No 2
>KOG0969|consensus
Probab=100.00 E-value=9.5e-35 Score=299.57 Aligned_cols=180 Identities=29% Similarity=0.584 Sum_probs=152.3
Q ss_pred cEEEEeeeeeecCCCCCCCCCccccccccccccCcEEEeeecCCCCceeEEEEeeccceeeeeCCCCCCccccccccccc
Q psy5919 2 FSMNIVTIDFFMSKPIAHFDPVHSELRNLVIQKVPVIRVFGNNIEGKKTCVFVHGVFPYLYIPFHHEPITETIVHSELRN 81 (387)
Q Consensus 2 ~~~~~~~~d~y~~~p~~~ld~~~~~~~~~~~~~vpvir~fG~t~~g~~~c~hvhg~~py~~~~~~~~~~~~~~v~s~lr~ 81 (387)
+.||++++|+|+.-|. ...+.|||+|+||+|.+|+|||||||||+|||||++|.+|.
T Consensus 75 i~fqq~~~e~y~~~~~------------~~~~~~pvvr~fGvT~~G~sv~~~v~gf~pyfYv~ap~g~~----------- 131 (1066)
T KOG0969|consen 75 IEFQQIDIEFYVENGS------------GTSGSVPVVRLFGVTKEGNSVCCHVHGFFPYFYVEAPNGFG----------- 131 (1066)
T ss_pred ceEEEeehhhhccCCC------------cccCCCceEEEeeeccCCCeEEEEEecccceEEecCCCCCC-----------
Confidence 5689999999998542 24568999999888888888888888888888888876652
Q ss_pred cccCCccEEEEEEecCCCCEEEEEEceeeeEEEEecCCCCchHHHHHHHHHHHHHHHHHHcCCCCCcceEEEEEEEEeec
Q psy5919 82 LVIQKVPVIRVFGNNVEGKKTCVFVHGVFPYLYIPFHHEPITETMLQQLAASIDKALNIALGYKDSVQHVFHISICKKFP 161 (387)
Q Consensus 82 ~~~~~~pvIrlFG~T~~G~svcv~Vhgf~PYfYv~~~~~~~~~~~l~~l~~~l~~~l~~s~~~~~~~~~V~~ie~V~~~~ 161 (387)
. .+|.++..+|+.++.. ..+.++++|++.+
T Consensus 132 -----------------------------------------~-e~i~~~~~~l~~~~~~--------~av~~ve~~~k~~ 161 (1066)
T KOG0969|consen 132 -----------------------------------------P-EHIGKFQQALDVKVTA--------HAVDHVEVVSKES 161 (1066)
T ss_pred -----------------------------------------H-HHHHHHHHHHHHHHHH--------hHHHHHHHHhhhh
Confidence 2 2677777777766542 3577889999999
Q ss_pred eecccC-CceEEEEEEecCcchHHHHHHHHhCCcccCC-----ccceeccCcchhhhhhhhcCCcceeeEEecceeEEec
Q psy5919 162 MYGYHA-DERTFLKILLYEPYHMSKLEDLLLNGAVFNE-----RFQPYESHIPYILQFCIDYNLYGMSNIEFNMVKFRSD 235 (387)
Q Consensus 162 ~YGY~~-~~~~FlKI~~~~P~~v~~l~~lL~~g~~~~~-----~~q~yEahIp~~lrFmiD~nL~G~~wi~~~~~~~r~~ 235 (387)
+|||++ ++.+|+||+...|..+.+++.+|++|..... .+++|||||+|.+|||+|.++.||+||++++++|+..
T Consensus 162 l~~~~g~~k~~f~kit~~lP~~~~~~r~~lergv~~~~~~~~~~~~~yEsNi~f~lrfmvd~~iVG~~wi~lp~gk~~~~ 241 (1066)
T KOG0969|consen 162 LYGYQGDTKQPFLKITVTLPRMVAAARRLLERGVFISGKGEKVGFTTYESNIDFVLRFMVDCDIVGMNWIELPAGKYRIR 241 (1066)
T ss_pred hheecCCCCceeEEEecccHHHHHHhHHHHHhcccccccCcceeeeEecCCccEEEEEEecCccccceeEEeccchheec
Confidence 999997 4789999999999999999999999944322 4789999999999999999999999999999999987
Q ss_pred CCCCCCCCCccceeeEeecccce
Q psy5919 236 SETSLPKLSHCQLEADVKAESIV 258 (387)
Q Consensus 236 ~~~~~~r~S~C~lEiDv~~~~Il 258 (387)
. .+.|+|++|+++.+.+++
T Consensus 242 ~----~~~s~cqlEv~v~y~~li 260 (1066)
T KOG0969|consen 242 D----NRVSRCQLEVSVNYKDLI 260 (1066)
T ss_pred c----chhcccceEEEEeecccc
Confidence 5 489999999999999998
No 3
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=99.93 E-value=1.9e-27 Score=219.88 Aligned_cols=133 Identities=29% Similarity=0.431 Sum_probs=122.4
Q ss_pred CCCcc-ceeeEeecccceeccccCCCccc--cchhHHHhhhHhhhhHHHhhhcCCCCCcccCcceeeeccc----hhhhh
Q psy5919 242 KLSHC-QLEADVKAESIVVDMAANDSDVA--TSGGITRYLSDVLLNSMRAILLGQEPHLLMDPDVYSMQDL----LDVKS 314 (387)
Q Consensus 242 r~S~C-~lEiDv~~~~Il~~~d~nr~~~~--~~~~L~~iw~de~~rr~~~~L~~~~~~~~~~~~Lys~~d~----~~~r~ 314 (387)
-++.| .-+..++|++|++||||.+++|+ +...|+.||++|.++..+ +||.||+.++. +.+|.
T Consensus 10 yC~~CH~~~~~vIParil~~WDf~~~pVs~~a~~~L~~~~~~Pl~~i~~-----------~np~ly~~v~~L~~v~~lR~ 78 (202)
T PF13901_consen 10 YCSSCHWNDTSVIPARILHNWDFRPYPVSRFAKQFLDQIWSKPLINIEA-----------LNPSLYSHVKELRKVRELRE 78 (202)
T ss_pred CCCCCCCCCceeccHHHHHhcCCCccHHHHHHHHHHHHhccCCEeeHHH-----------hCHHHHHHhHHHHHHHHHHH
Confidence 48889 55889999999999999999985 678899999999999999 99999998854 45899
Q ss_pred hhhhHHHHHHHHhhhhHH-HHHhhhcCCCccccCCCcCChhhHHhccccccHHHHHHHHHHhhccccccccCCC
Q psy5919 315 GALYLKLKDLVSACSIFR-MRAILLGQEPHLLMDPDVYSMQDLLDVKSGALYLKLKDLVSACSSHVYNCEPTNA 387 (387)
Q Consensus 315 ~l~~~~lk~~l~tCr~~~-~~~~~~~~~~hl~~~~~~yS~~Dl~~v~~G~l~~~l~~l~~~~~~Hv~~C~lC~~ 387 (387)
+|. +|++||.+||.+. +...+.+.+.||++|+|+|||+||++|++|.|.++|+++++.+.+||.+|++|+|
T Consensus 79 ~L~--~l~~yl~~C~~~~~~~~~~~~~~~hl~~~~~~YSl~DL~~v~~G~L~~~L~~l~~~~~~HV~~C~lC~~ 150 (202)
T PF13901_consen 79 QLS--LLKDYLRTCRSADSLKLQLRQPRDHLLEDPHLYSLADLVQVKSGQLLPQLEKLVQFAEKHVYSCELCQQ 150 (202)
T ss_pred HHH--HHHHHHHhChHHHHHHhhhccchhhhhhCCceEcHHHHHHHhhchHHHHHHHHHHHHHHHHHHhHHHHh
Confidence 999 9999999999998 5555669999999999999999999999999999999999999999999999986
No 4
>KOG0968|consensus
Probab=99.90 E-value=4.6e-25 Score=234.93 Aligned_cols=202 Identities=30% Similarity=0.478 Sum_probs=157.5
Q ss_pred CcEEEeeecCCCCceeEEEEeeccceeeeeCCCCCCccccccccccccccCCccEEEEEEecCCCCEEEEEEceeeeEEE
Q psy5919 35 VPVIRVFGNNIEGKKTCVFVHGVFPYLYIPFHHEPITETIVHSELRNLVIQKVPVIRVFGNNVEGKKTCVFVHGVFPYLY 114 (387)
Q Consensus 35 vpvir~fG~t~~g~~~c~hvhg~~py~~~~~~~~~~~~~~v~s~lr~~~~~~~pvIrlFG~T~~G~svcv~Vhgf~PYfY 114 (387)
-||+|+||+..+|+.+|||+||++||+|+.|++.- +++ -+++|.
T Consensus 49 tqv~~v~~a~~~g~~~~~~s~g~l~~i~~k~d~~~-t~t-----------------------------~l~~~d------ 92 (1488)
T KOG0968|consen 49 TQVIRVFGANEEGETVCCFSHGVLPYIYVKYDSFA-TTT-----------------------------DLEVPD------ 92 (1488)
T ss_pred Cccceecccccccceeeeeecccchhhhhhhhhhc-ccc-----------------------------cccccc------
Confidence 35888999999999999999999999999997432 111 122222
Q ss_pred EecCCCCchHHHHHHHHHHHHHHHHHHcCCCC-----CcceEEEEEEEEeeceecccCCceEEEEEEecCcchHHHHHHH
Q psy5919 115 IPFHHEPITETMLQQLAASIDKALNIALGYKD-----SVQHVFHISICKKFPMYGYHADERTFLKILLYEPYHMSKLEDL 189 (387)
Q Consensus 115 v~~~~~~~~~~~l~~l~~~l~~~l~~s~~~~~-----~~~~V~~ie~V~~~~~YGY~~~~~~FlKI~~~~P~~v~~l~~l 189 (387)
.+.|+...++.++..+..... ....|.++++|+++|||||+..+..|+||++.+|+-..++.++
T Consensus 93 -----------~~aqi~k~le~a~~~~~~a~~esq~~~~~~v~sv~~vk~~p~~~~~~~~s~~~k~~l~~~sck~rl~el 161 (1488)
T KOG0968|consen 93 -----------FLAQIQKSLEYALALAARANPESQKPNLNAVQSVQLVKGIPFYGYSFCFSKFLKICLFSPSCKDRLVEL 161 (1488)
T ss_pred -----------HHHHHHHHHHHHHHHHhhcChhhhcchHHHHHHHHhcCCCCccccccchhhHHHHHhcCchhHHHHHHH
Confidence 456777777777665543211 2346889999999999999999999999999999999999999
Q ss_pred HhCCcccCCccceeccCcchhhhhhhhcCCcceeeEEecceeEEecCCCCCCCCCccceeeEeecc-ccee-ccccCCCc
Q psy5919 190 LLNGAVFNERFQPYESHIPYILQFCIDYNLYGMSNIEFNMVKFRSDSETSLPKLSHCQLEADVKAE-SIVV-DMAANDSD 267 (387)
Q Consensus 190 L~~g~~~~~~~q~yEahIp~~lrFmiD~nL~G~~wi~~~~~~~r~~~~~~~~r~S~C~lEiDv~~~-~Il~-~~d~nr~~ 267 (387)
+++|++.++.+++||+|+||.+|||+|.|++||.||+++...++.+.++ ...|..++.+... .++. -|...+-.
T Consensus 162 ~rdg~ipnk~is~~esh~~y~~~r~~d~n~~~~~~ikvds~~~~n~~dn----sv~d~~p~t~sdn~~l~ds~~~s~kl~ 237 (1488)
T KOG0968|consen 162 FRDGAIPNKVISVYESHLPYLLQRMVDHNLYGCAPIKVDSSIIKNDVDN----SVFDNVPVTVSDNLALLDSCWLSEKLI 237 (1488)
T ss_pred HhcccCCCcccccchhccchhhhhhhhcccccceeeecchhhhcCCccc----ccccCcceeeCccHHHHhhcCchhccC
Confidence 9999999999999999999999999999999999999999999887543 5567777777765 3331 22211111
Q ss_pred c--------c-----cchhHHHhhhHhhhhHHH
Q psy5919 268 V--------A-----TSGGITRYLSDVLLNSMR 287 (387)
Q Consensus 268 ~--------~-----~~~~L~~iw~de~~rr~~ 287 (387)
. . ...+++.+|+|++..|..
T Consensus 238 ~t~lsd~~~~~~~~~~I~~l~e~~kd~~kcrn~ 270 (1488)
T KOG0968|consen 238 HTDLSDTPASSPNSLLITSLAEIWKDEAKCRNL 270 (1488)
T ss_pred cchhhhccccCCCcceeeehHHhhhhHHHhhcc
Confidence 0 1 235699999999987554
No 5
>KOG1829|consensus
Probab=99.87 E-value=4.1e-23 Score=213.33 Aligned_cols=133 Identities=21% Similarity=0.351 Sum_probs=123.6
Q ss_pred CCCcc-ceeeEeecccceeccccCCCccc--cchhHHHhhhHhhhhHHHhhhcCCCCCcccCcceeeeccchh----hhh
Q psy5919 242 KLSHC-QLEADVKAESIVVDMAANDSDVA--TSGGITRYLSDVLLNSMRAILLGQEPHLLMDPDVYSMQDLLD----VKS 314 (387)
Q Consensus 242 r~S~C-~lEiDv~~~~Il~~~d~nr~~~~--~~~~L~~iw~de~~rr~~~~L~~~~~~~~~~~~Lys~~d~~~----~r~ 314 (387)
-|+.| +-+.-++|++|+++|||++++++ ..+.|++||+.|.++.+. +|+.||+++++|+ +|.
T Consensus 368 ~C~~Ch~~~~svIPARVl~~WDf~~y~Vs~~a~~~L~~ir~~Pl~~~q~-----------ln~~Ly~~~~~L~~v~~lR~ 436 (580)
T KOG1829|consen 368 FCDCCHQNDKSVIPARVLHNWDFTKYPVSNFAKQFLDEIREQPLFNLQD-----------LNPDLYSKVKALAEVKELRQ 436 (580)
T ss_pred hCchhcccCcccccccceecccCcccccchhHHHHHHHHhccchhhhcc-----------cChHHHhhhHHHHHHHHHHH
Confidence 37788 77889999999999999999986 678999999999999999 9999999998764 799
Q ss_pred hhhhHHHHHHHHhhhhHH--HHHhhhcCCCccccCCCcCChhhHHhccccccHHHHHHHHHHhhccccccccCCC
Q psy5919 315 GALYLKLKDLVSACSIFR--MRAILLGQEPHLLMDPDVYSMQDLLDVKSGALYLKLKDLVSACSSHVYNCEPTNA 387 (387)
Q Consensus 315 ~l~~~~lk~~l~tCr~~~--~~~~~~~~~~hl~~~~~~yS~~Dl~~v~~G~l~~~l~~l~~~~~~Hv~~C~lC~~ 387 (387)
+|. +|+.|+++||++. ....+...++||++++|+|||+||.+|++|.|...|+++++.+.+||.+|.+|.+
T Consensus 437 qL~--~m~~~l~~Cr~a~~~~~~~~~~~~~yL~e~~~~~Sl~DL~~i~~g~L~~~l~~~~k~~~~HV~~C~lC~~ 509 (580)
T KOG1829|consen 437 QLQ--HIEGYLKTCRFASLKLLRQRLAVRRYLTESPHLFSLKDLQDIQDGALLRLLNELTKLSSKHVKECDLCTG 509 (580)
T ss_pred HHH--HHHHHHHhhhcchhhhhhhhhhhhhhhccCchhhhhhhHHHhhcccHHHHHHHHHHHhhhhhhhchhhcc
Confidence 999 9999999999996 5556678999999999999999999999999999999999999999999999975
No 6
>PF03104 DNA_pol_B_exo1: DNA polymerase family B, exonuclease domain Several related DNA polymerases were too dissimilar to be included.; InterPro: IPR006133 DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases 2.7.7.7 from EC) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known. However, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold [].; GO: 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 4AHC_A 3A2F_A 2JGU_A 4AIL_C 1NOY_A 1NOZ_B 3IAY_A 1WNS_A 3K5O_A ....
Probab=99.81 E-value=1.3e-20 Score=184.53 Aligned_cols=145 Identities=30% Similarity=0.479 Sum_probs=113.9
Q ss_pred ecCCCCEEEEEEceeeeEEEEecCCCCchHHHHHHHHHHHHHHHHHHcCCCCCcceEEEEEEEEe-eceecccCCceEEE
Q psy5919 95 NNVEGKKTCVFVHGVFPYLYIPFHHEPITETMLQQLAASIDKALNIALGYKDSVQHVFHISICKK-FPMYGYHADERTFL 173 (387)
Q Consensus 95 ~T~~G~svcv~Vhgf~PYfYv~~~~~~~~~~~l~~l~~~l~~~l~~s~~~~~~~~~V~~ie~V~~-~~~YGY~~~~~~Fl 173 (387)
.|++|+|||++|+||+||||+..++..... .+. +.+++. ... .....+.+++.|++ ++||||+.++..|+
T Consensus 1 ~t~~g~svcv~v~~f~pyfYv~~~~~~~~~-~~~---~~~~~~----~~~-~~~~~~~~~~~V~r~~~~~~y~~~~~~~l 71 (325)
T PF03104_consen 1 MTEDGKSVCVRVHGFRPYFYVLPPESDSPK-DLE---QFIEQL----LRK-KFKIDVFKIEKVKRKKSFYGYDGKEEPFL 71 (325)
T ss_dssp -ECTSEEEEEEEST--EEEEEEESSGGGHH-HHT---THEEHH----EET-TEEEEEEEEEEEEEEEESSEETTEEEEEE
T ss_pred CCCCCCEEEEEEcCCCEEEEEECCCCccHH-HHH---HHHHHH----hhh-ccCCceEEEEEEEeeeeeccCCCCCceEE
Confidence 489999999999999999999999865332 111 111110 111 13568899999999 99999999888899
Q ss_pred EEEecCcchHHHHHHHHhCCcccCCccceeccCcchhhhhhhhcCCcceeeEEecceeEEecCCCCCCCCCccceeeEee
Q psy5919 174 KILLYEPYHMSKLEDLLLNGAVFNERFQPYESHIPYILQFCIDYNLYGMSNIEFNMVKFRSDSETSLPKLSHCQLEADVK 253 (387)
Q Consensus 174 KI~~~~P~~v~~l~~lL~~g~~~~~~~q~yEahIp~~lrFmiD~nL~G~~wi~~~~~~~r~~~~~~~~r~S~C~lEiDv~ 253 (387)
||++.+|..++++++.|++ ..+++||+||++++|||+|+||.|++|++++....... .+.|+|+.|+++.
T Consensus 72 kV~~~~~~~~~~~~~~l~~-----~~~~~~e~~i~~~~rfl~~~~i~~~~wi~i~~~~~~~~-----~~~s~~~~e~~~~ 141 (325)
T PF03104_consen 72 KVYFSSPRDVRKLRDNLKK-----TFFKVYEADIPPLERFLIDRNIRGPGWIKIKNPSKPVK-----DRVSWCDIEFSVD 141 (325)
T ss_dssp EEEESSTTHHHHHHHHHHH-----TEEEEESTSS-HHHHHHHHTTHCTTEEEEEETTECHHH-----HHTCTCSCECECC
T ss_pred EEEECcHHHHHHHHHHHHh-----ccchhhccCCCHHHheeeecCcccceeeeccccccccc-----ccccccccccccc
Confidence 9999999999999999985 46899999999999999999999999999988722211 3688899999988
Q ss_pred cccce
Q psy5919 254 AESIV 258 (387)
Q Consensus 254 ~~~Il 258 (387)
+.++.
T Consensus 142 ~~~~~ 146 (325)
T PF03104_consen 142 YSNLK 146 (325)
T ss_dssp HHHHE
T ss_pred ccccc
Confidence 88877
No 7
>PRK05761 DNA polymerase I; Reviewed
Probab=99.48 E-value=1.1e-13 Score=151.07 Aligned_cols=124 Identities=15% Similarity=0.203 Sum_probs=99.9
Q ss_pred cCCccEEEEEEecCCCCEEEEEEc-eeeeEEEEecCCCCchHHHHHHHHHHHHHHHHHHcCCCCCcceEEEEEEEEeece
Q psy5919 84 IQKVPVIRVFGNNVEGKKTCVFVH-GVFPYLYIPFHHEPITETMLQQLAASIDKALNIALGYKDSVQHVFHISICKKFPM 162 (387)
Q Consensus 84 ~~~~pvIrlFG~T~~G~svcv~Vh-gf~PYfYv~~~~~~~~~~~l~~l~~~l~~~l~~s~~~~~~~~~V~~ie~V~~~~~ 162 (387)
..+.|+|++||.+ +|+.+.+.-. ||.||||+..++.. +.+. + ... ....+..+++|++.+.
T Consensus 29 ~~~~~vi~l~~~~-~~~~~~~~d~~gfkPYfy~~~~~~~-----~~~~---~------~~~---~~~~~~~~e~~~~~~~ 90 (787)
T PRK05761 29 KLGKAVVKLYDPE-TGKIYKWYDRTGHKPYFLTDLDPDE-----IDKI---P------KIL---RHPSFDHLEIVEKYDG 90 (787)
T ss_pred cCCeeEEEEEecC-CCeEEEEEcCCCCCCeEEecCChHH-----HHhh---h------hhh---cCCCeeeEEEEEEEec
Confidence 4578999999996 6776666665 59999999876532 1110 0 000 1356889999999998
Q ss_pred ecccCCceEEEEEEecCcchHHHHHHHHhCCcccCCccceeccCcchhhhhhhhcCCcceeeEEecceeEE
Q psy5919 163 YGYHADERTFLKILLYEPYHMSKLEDLLLNGAVFNERFQPYESHIPYILQFCIDYNLYGMSNIEFNMVKFR 233 (387)
Q Consensus 163 YGY~~~~~~FlKI~~~~P~~v~~l~~lL~~g~~~~~~~q~yEahIp~~lrFmiD~nL~G~~wi~~~~~~~r 233 (387)
|+|+ +.+++||++.+|..++++|+.++++ +++|||+|+|.+|||+|++|.||+|+.+.+...+
T Consensus 91 ~~~~--~~~~~kI~~~~p~~v~~~r~~~~~~------~~~~EaDI~f~~RyliD~~i~~~~~~~~~~~~~~ 153 (787)
T PRK05761 91 LRDK--KVKVTKIVVKDPLAVRRLRLSVRDI------PRAWEADIKYEFRYIYDNGLIPGMPYDVKNGLES 153 (787)
T ss_pred cCCC--cceEEEEEECCHHHHHHHHHHHHhh------hhheeCCCChHHheEEeCCCCCCceEEecccccc
Confidence 8875 6899999999999999999999874 6899999999999999999999999999776543
No 8
>PRK05762 DNA polymerase II; Reviewed
Probab=99.34 E-value=3e-12 Score=140.29 Aligned_cols=115 Identities=13% Similarity=0.192 Sum_probs=88.2
Q ss_pred cCCccEEEEEEecCCCCEEEEEEceeeeEEEEecCCCCchHHHHHHHHHHHHHHHHHHcCCCCCcceEEEEEEEEeecee
Q psy5919 84 IQKVPVIRVFGNNVEGKKTCVFVHGVFPYLYIPFHHEPITETMLQQLAASIDKALNIALGYKDSVQHVFHISICKKFPMY 163 (387)
Q Consensus 84 ~~~~pvIrlFG~T~~G~svcv~Vhgf~PYfYv~~~~~~~~~~~l~~l~~~l~~~l~~s~~~~~~~~~V~~ie~V~~~~~Y 163 (387)
.+.+|+||+||+|++|.++|+++.||.||||+..+..... ..+.. . . ...++.+ ++.
T Consensus 16 ~~~~~vi~l~g~t~~G~~~~v~~~~~~~yFy~~~~~~~~~--------~~~~~----~------~--~~~~~~~---~l~ 72 (786)
T PRK05762 16 TPGGPEVELWLATDEGPRVVLLDPQFRPYFIPAEQDERAE--------SLLAG----E------I--GVRLSPL---ALK 72 (786)
T ss_pred ECCeEEEEEEEEcCCCCEEEEECCCCcEEEEEeCchhhhH--------HHHhh----c------c--cceeecc---cee
Confidence 4678999999999999999999999999999985542211 11111 0 0 0223333 333
Q ss_pred cccCCceEEEEEEecCcchHHHHHHHHhCCcccCCccceeccCcchhhhhhhhcCCcceeeEEec
Q psy5919 164 GYHADERTFLKILLYEPYHMSKLEDLLLNGAVFNERFQPYESHIPYILQFCIDYNLYGMSNIEFN 228 (387)
Q Consensus 164 GY~~~~~~FlKI~~~~P~~v~~l~~lL~~g~~~~~~~q~yEahIp~~lrFmiD~nL~G~~wi~~~ 228 (387)
.|.+ +++..+++.+++.+.++++.+++ ..+++|||+|+|.+|||+|.+|.||+|+...
T Consensus 73 ~~~~--~~~~~~~~~~~~~~~~~~~~~~~-----~~~~i~EaDI~~~~R~lid~~i~~~~w~~~~ 130 (786)
T PRK05762 73 DFHR--RPVLGLYCRQHRQLTRLPKRLRE-----GGVDVYEADIRFPERYLMERFITPCVWFSGE 130 (786)
T ss_pred cccC--CeeeEEEeccHHHHHHHHHHHHH-----cCCeEEECCCChhHhheeeCCCCCcEEEEEE
Confidence 3332 35778899999999999999987 4799999999999999999999999999764
No 9
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=98.89 E-value=7.3e-09 Score=113.83 Aligned_cols=129 Identities=20% Similarity=0.348 Sum_probs=95.4
Q ss_pred CCccEEEEEEecCCCCEEEEEEceeeeEEEEecCCCCchHHHHHHHHHHHHHHHHHHcCCCCCcceEEEEEEEEeeceec
Q psy5919 85 QKVPVIRVFGNNVEGKKTCVFVHGVFPYLYIPFHHEPITETMLQQLAASIDKALNIALGYKDSVQHVFHISICKKFPMYG 164 (387)
Q Consensus 85 ~~~pvIrlFG~T~~G~svcv~Vhgf~PYfYv~~~~~~~~~~~l~~l~~~l~~~l~~s~~~~~~~~~V~~ie~V~~~~~YG 164 (387)
.+.|++++||.+++|++++..+-+|.||||+..++....+ .+ .+ ..... ........+.+. ..+.
T Consensus 6 ~~~~~~~~~~~~~~G~~v~~~~~~~~~~~~~~~~~~~~~~-~~-------~~----~~~~~-~~~~~~~~~~~~--~~~~ 70 (792)
T COG0417 6 DGFPLVRIFGDTDSGKSVVKLVATFRPYFYVTLDNSRPED-YV-------LK----ILNRR-LDDVLELEEVEN--VPDP 70 (792)
T ss_pred cCceEEEEeeecCCCCEEEEEecCCCCcEEEecCCCcccc-hh-------hh----hcccc-ccccceeeeeee--eecc
Confidence 4589999999999999999999999999999999862221 11 00 00000 011112222222 3334
Q ss_pred ccCCceEEEEEEecCcchHHHHHHHHhCCcccCCccceeccCcchhhhhhhhcCCcceeeEEecce
Q psy5919 165 YHADERTFLKILLYEPYHMSKLEDLLLNGAVFNERFQPYESHIPYILQFCIDYNLYGMSNIEFNMV 230 (387)
Q Consensus 165 Y~~~~~~FlKI~~~~P~~v~~l~~lL~~g~~~~~~~q~yEahIp~~lrFmiD~nL~G~~wi~~~~~ 230 (387)
|...+....||+...|..++++++.... .......+||++|||.+|||+|+++++|.|+.++..
T Consensus 71 ~~~~~~~~~~i~~~~p~~v~~~r~~~~~--~~~~~~~i~e~dI~~~~r~~~d~~i~~~~~~~~~~~ 134 (792)
T COG0417 71 YLGREVEVLKIYARDPQAVRKLREKVKR--ELEGVVDIFEADIPFAMRYLIDKGIRPMVWVSVDVE 134 (792)
T ss_pred ccCCcccceeeEecCHHHHHHHHHHHhh--hhhccceEeecCCCcchheeeecCCCCceEEEeeec
Confidence 5567788999999999999999999885 233468999999999999999999999999998744
No 10
>KOG0969|consensus
Probab=98.82 E-value=3.1e-09 Score=111.89 Aligned_cols=39 Identities=41% Similarity=0.847 Sum_probs=35.7
Q ss_pred ccccCCccEEEEEEecCCCCEEEEEEceeeeEEEEecCC
Q psy5919 81 NLVIQKVPVIRVFGNNVEGKKTCVFVHGVFPYLYIPFHH 119 (387)
Q Consensus 81 ~~~~~~~pvIrlFG~T~~G~svcv~Vhgf~PYfYv~~~~ 119 (387)
+..+.++|+||+||+|.+|+|||||||||+||||+++|.
T Consensus 90 ~~~~~~~pvvr~fGvT~~G~sv~~~v~gf~pyfYv~ap~ 128 (1066)
T KOG0969|consen 90 SGTSGSVPVVRLFGVTKEGNSVCCHVHGFFPYFYVEAPN 128 (1066)
T ss_pred CcccCCCceEEEeeeccCCCeEEEEEecccceEEecCCC
Confidence 345678999999999999999999999999999999884
No 11
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=97.80 E-value=2.2e-05 Score=88.95 Aligned_cols=62 Identities=27% Similarity=0.506 Sum_probs=54.9
Q ss_pred cEEEEeeeeee------cCCCCCCCCCccccccccccccCcEEEeeecCCCCceeEEEEeeccceeeeeCCCCCC
Q psy5919 2 FSMNIVTIDFF------MSKPIAHFDPVHSELRNLVIQKVPVIRVFGNNIEGKKTCVFVHGVFPYLYIPFHHEPI 70 (387)
Q Consensus 2 ~~~~~~~~d~y------~~~p~~~ld~~~~~~~~~~~~~vpvir~fG~t~~g~~~c~hvhg~~py~~~~~~~~~~ 70 (387)
+.||++++||| ++.|.+ .+++...+.|||||+||.|.+|+|||||||||.|||||++|+++.
T Consensus 42 ~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~pvIRlFGvTe~G~SV~v~V~gF~PYFYV~~p~~~~ 109 (1054)
T PTZ00166 42 LVFFQLDADYTEKDDKSQGNPHN-------TVSGVRHVEVPIIRLYGVTKEGHSVLVNVHNFFPYFYIEAPPNFL 109 (1054)
T ss_pred ceEEEEeeeccccccccccCccc-------cCCCccCCCceEEEEEEecCCCCEEEEEEeCCceEEEEecCCCCC
Confidence 57999999999 565544 466777889999999999999999999999999999999999885
No 12
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=97.38 E-value=0.00017 Score=66.99 Aligned_cols=58 Identities=34% Similarity=0.422 Sum_probs=54.0
Q ss_pred hcCCCCCcccCcceeeeccchhhhhhhhhHHHHHHHHhhhhHHHHHhhhcCCCccccC
Q psy5919 290 LLGQEPHLLMDPDVYSMQDLLDVKSGALYLKLKDLVSACSIFRMRAILLGQEPHLLMD 347 (387)
Q Consensus 290 L~~~~~~~~~~~~Lys~~d~~~~r~~l~~~~lk~~l~tCr~~~~~~~~~~~~~hl~~~ 347 (387)
+...+.|++.++++||++||.++++|-+.+.|++++..+..|+..|.+|+.+||+||-
T Consensus 100 ~~~~~~hl~~~~~~YSl~DL~~v~~G~L~~~L~~l~~~~~~HV~~C~lC~~kGfiCe~ 157 (202)
T PF13901_consen 100 LRQPRDHLLEDPHLYSLADLVQVKSGQLLPQLEKLVQFAEKHVYSCELCQQKGFICEI 157 (202)
T ss_pred hccchhhhhhCCceEcHHHHHHHhhchHHHHHHHHHHHHHHHHHHhHHHHhCCCCCcc
Confidence 3477899999999999999999999999999999999999999999999999999974
No 13
>KOG1798|consensus
Probab=97.20 E-value=0.00094 Score=75.53 Aligned_cols=127 Identities=15% Similarity=0.185 Sum_probs=93.8
Q ss_pred ccEEEEEEecCCCCEEEEEEceeeeEEEEecCCCCchHHHHHHHHHHHHHHHHHHcCCCCCcceEEEEEEEEeeceeccc
Q psy5919 87 VPVIRVFGNNVEGKKTCVFVHGVFPYLYIPFHHEPITETMLQQLAASIDKALNIALGYKDSVQHVFHISICKKFPMYGYH 166 (387)
Q Consensus 87 ~pvIrlFG~T~~G~svcv~Vhgf~PYfYv~~~~~~~~~~~l~~l~~~l~~~l~~s~~~~~~~~~V~~ie~V~~~~~YGY~ 166 (387)
.-.+-+|=.+.+|.+--+.+ -|+|||||.+-++...+ ..+ .|...+ ...+++||.|.|..+.=++
T Consensus 69 ~S~VD~yFi~~dG~~Fk~~~-py~PYFyiAt~d~~e~~-----Ve~----yL~Kky-----~g~i~~ie~v~kEDL~lkN 133 (2173)
T KOG1798|consen 69 ISAVDLYFIDDDGSSFKVKY-PYRPYFYIATRDGMELE-----VEE----YLRKKY-----EGQIADIEIVHKEDLDLKN 133 (2173)
T ss_pred eeEEEEEEEccCCCeEEEee-cccceEEEeeccccHHH-----HHH----HHHHHH-----hhhhhheeEecHhhcCchh
Confidence 34678899999999999988 69999999988753221 222 232222 2357889999999987776
Q ss_pred --CC-ceEEEEEEecCcchHHHHHHHHhC----C----------------ccc--------CCccceeccCcchhhhhhh
Q psy5919 167 --AD-ERTFLKILLYEPYHMSKLEDLLLN----G----------------AVF--------NERFQPYESHIPYILQFCI 215 (387)
Q Consensus 167 --~~-~~~FlKI~~~~P~~v~~l~~lL~~----g----------------~~~--------~~~~q~yEahIp~~lrFmi 215 (387)
.| +..|+|++|.+-...-+++..|.. . ... +....+-|-+|||..|+.|
T Consensus 134 HLsGlqk~yiKlsF~t~~~L~~vrK~l~~iV~~N~~q~~a~daY~~~ls~~~~~~~q~D~ld~IvDiREYDVPyHvR~sI 213 (2173)
T KOG1798|consen 134 HLSGLQKTYIKLSFDTVNQLVEVRKDLRPIVKRNKAQFDALDAYTNILSGNLNGRDQGDALDSIVDIREYDVPYHVRVSI 213 (2173)
T ss_pred hhhcccccEEEEEEecHHHHHHHHHHHHHHHHhhhhhhhhHHHHHHHHhhhccCCcccchHhhhhhHhhcCCceEEEEee
Confidence 34 579999999988877666655432 1 111 1135688999999999999
Q ss_pred hcCCcceeeEEec
Q psy5919 216 DYNLYGMSNIEFN 228 (387)
Q Consensus 216 D~nL~G~~wi~~~ 228 (387)
|.+|.-.-|+.+.
T Consensus 214 D~~IrvG~WY~V~ 226 (2173)
T KOG1798|consen 214 DLDIRVGQWYNVS 226 (2173)
T ss_pred cCCeeeeeeeeee
Confidence 9999999999987
No 14
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.05 E-value=0.0064 Score=70.13 Aligned_cols=160 Identities=19% Similarity=0.272 Sum_probs=98.9
Q ss_pred CccEEEEEEecCCCCEEEEEEceee-eEEEEecCCCCchHH--HHH---HHHHHHHHHHH-HHcCCCCCcceEEEEEEEE
Q psy5919 86 KVPVIRVFGNNVEGKKTCVFVHGVF-PYLYIPFHHEPITET--MLQ---QLAASIDKALN-IALGYKDSVQHVFHISICK 158 (387)
Q Consensus 86 ~~pvIrlFG~T~~G~svcv~Vhgf~-PYfYv~~~~~~~~~~--~l~---~l~~~l~~~l~-~s~~~~~~~~~V~~ie~V~ 158 (387)
...++.+||+..+|.++|+.|.|+. ..|+++.++....+. .+. .+..--.+..+ ..++.. ..-.+...|.
T Consensus 321 ~~G~~~lfGr~~~~~s~~~~v~g~~R~~~~l~~~Grv~~D~~~~~~~~~~l~~y~le~vs~~~lg~~---k~dv~~k~I~ 397 (1172)
T TIGR00592 321 KLGVVLLFGRDVDHVSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYK---KEKFRAKPIA 397 (1172)
T ss_pred CCCeEEEecccCCceeEEEEECCeeeeeEEeeccccccccccchhcccccHHHHHHHHHHHHHhhcC---cCceeeEEeh
Confidence 3467899999777899999999976 889999887322110 000 01110001111 111211 1111112222
Q ss_pred eeceecccC------CceEEEEEEecCcchHHHHHHHHhCCcccCCccceeccCcchhhhhhhhcCCcceeeEEecceeE
Q psy5919 159 KFPMYGYHA------DERTFLKILLYEPYHMSKLEDLLLNGAVFNERFQPYESHIPYILQFCIDYNLYGMSNIEFNMVKF 232 (387)
Q Consensus 159 ~~~~YGY~~------~~~~FlKI~~~~P~~v~~l~~lL~~g~~~~~~~q~yEahIp~~lrFmiD~nL~G~~wi~~~~~~~ 232 (387)
+ .|-+.. ....++|+.+..+..+..+..+.... .......+|+++.....||+++.++.|++|+.+.....
T Consensus 398 ~--~~~~~~~~~~v~y~~~~lkv~y~l~~~~~~l~~l~~~~-~g~~~~~vf~~n~g~~erfll~rki~gp~WL~i~~p~~ 474 (1172)
T TIGR00592 398 K--KYEFEAPDIDAPYSSEYLEVTYELGKEFAPMEALPSDL-KGQTFWHVFGSNTGNLERFLLLRKIKGPCWLAVKGPDE 474 (1172)
T ss_pred h--hccCCCCccCCcCCcceEEEEEccCccchhhhhhhhhc-cCCcchheeccCHHHHHHHHhcCCCCCCceEEeCCCcc
Confidence 1 121221 12478999999887777777666531 11233579999999999999999999999999987765
Q ss_pred EecCCCCCCCCCccceeeEeeccc
Q psy5919 233 RSDSETSLPKLSHCQLEADVKAES 256 (387)
Q Consensus 233 r~~~~~~~~r~S~C~lEiDv~~~~ 256 (387)
+.. .+.|.|.+|..+....
T Consensus 475 ~~~-----~~~S~c~yEga~v~~p 493 (1172)
T TIGR00592 475 LEY-----PRRSWCKYEGGYVKPP 493 (1172)
T ss_pred cCc-----CCccccceEEEEecCc
Confidence 432 2478999999977665
No 15
>PF03104 DNA_pol_B_exo1: DNA polymerase family B, exonuclease domain Several related DNA polymerases were too dissimilar to be included.; InterPro: IPR006133 DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases 2.7.7.7 from EC) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known. However, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold [].; GO: 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 4AHC_A 3A2F_A 2JGU_A 4AIL_C 1NOY_A 1NOZ_B 3IAY_A 1WNS_A 3K5O_A ....
Probab=96.11 E-value=0.0027 Score=62.10 Aligned_cols=27 Identities=37% Similarity=0.669 Sum_probs=22.3
Q ss_pred CCCCceeEEEEeeccceeeeeCCCCCC
Q psy5919 44 NIEGKKTCVFVHGVFPYLYIPFHHEPI 70 (387)
Q Consensus 44 t~~g~~~c~hvhg~~py~~~~~~~~~~ 70 (387)
|.+|++||+|||||.||||+..+.+..
T Consensus 2 t~~g~svcv~v~~f~pyfYv~~~~~~~ 28 (325)
T PF03104_consen 2 TEDGKSVCVRVHGFRPYFYVLPPESDS 28 (325)
T ss_dssp ECTSEEEEEEEST--EEEEEEESSGGG
T ss_pred CCCCCEEEEEEcCCCEEEEEECCCCcc
Confidence 789999999999999999999986653
No 16
>PRK05762 DNA polymerase II; Reviewed
Probab=95.99 E-value=0.0085 Score=66.45 Aligned_cols=49 Identities=16% Similarity=0.158 Sum_probs=40.3
Q ss_pred cEEEEeeeeeecCCCCCCCCCccccccccccccCcEEEeeecCCCCceeEEEEeeccceeeeeCCCC
Q psy5919 2 FSMNIVTIDFFMSKPIAHFDPVHSELRNLVIQKVPVIRVFGNNIEGKKTCVFVHGVFPYLYIPFHHE 68 (387)
Q Consensus 2 ~~~~~~~~d~y~~~p~~~ld~~~~~~~~~~~~~vpvir~fG~t~~g~~~c~hvhg~~py~~~~~~~~ 68 (387)
+.+++++.||.... .-||||+||.|.+|.++|+++.|+-||||+..+.+
T Consensus 4 ~~~~lL~~~~~~~~------------------~~~vi~l~g~t~~G~~~~v~~~~~~~yFy~~~~~~ 52 (786)
T PRK05762 4 QQGFILTRHYRDTP------------------GGPEVELWLATDEGPRVVLLDPQFRPYFIPAEQDE 52 (786)
T ss_pred eEEEEEeeEEEEEC------------------CeEEEEEEEEcCCCCEEEEECCCCcEEEEEeCchh
Confidence 45677777777531 23999999999999999999999999999987653
No 17
>KOG0968|consensus
Probab=95.15 E-value=0.0095 Score=66.35 Aligned_cols=59 Identities=42% Similarity=0.776 Sum_probs=46.8
Q ss_pred CCccEEEEEEecCCCCEEEEEEceeeeEEEEecCCCCc-hHHHHHHHHHHHHHHHHHHcC
Q psy5919 85 QKVPVIRVFGNNVEGKKTCVFVHGVFPYLYIPFHHEPI-TETMLQQLAASIDKALNIALG 143 (387)
Q Consensus 85 ~~~pvIrlFG~T~~G~svcv~Vhgf~PYfYv~~~~~~~-~~~~l~~l~~~l~~~l~~s~~ 143 (387)
...+|+++||..++|+.+|+++||.+||+|+.+++... ..-...++.+.+.+.++-+..
T Consensus 47 q~tqv~~v~~a~~~g~~~~~~s~g~l~~i~~k~d~~~t~t~l~~~d~~aqi~k~le~a~~ 106 (1488)
T KOG0968|consen 47 QPTQVIRVFGANEEGETVCCFSHGVLPYIYVKYDSFATTTDLEVPDFLAQIQKSLEYALA 106 (1488)
T ss_pred CCCccceecccccccceeeeeecccchhhhhhhhhhccccccccccHHHHHHHHHHHHHH
Confidence 45679999999999999999999999999999988432 222455677888887776654
No 18
>KOG0970|consensus
Probab=93.66 E-value=0.22 Score=55.94 Aligned_cols=152 Identities=19% Similarity=0.315 Sum_probs=88.5
Q ss_pred cEEEEEEe----cCCCCEEEEEEceeeeEEEE-ecCCCC-------chHHHHHHHHHHHHHHHHHHcCCCCCcceEEEEE
Q psy5919 88 PVIRVFGN----NVEGKKTCVFVHGVFPYLYI-PFHHEP-------ITETMLQQLAASIDKALNIALGYKDSVQHVFHIS 155 (387)
Q Consensus 88 pvIrlFG~----T~~G~svcv~Vhgf~PYfYv-~~~~~~-------~~~~~l~~l~~~l~~~l~~s~~~~~~~~~V~~ie 155 (387)
-++-+||+ ++.+.|||+.|.|..=-.|+ |-|... ........+...+...+...++-.. .+..
T Consensus 349 g~l~LFGKVk~~~~t~~Sccv~V~ni~R~lyflPR~~~l~~~~~e~~~~~s~~dv~~E~~~~l~~k~~~~~-----fk~k 423 (1429)
T KOG0970|consen 349 GTLYLFGKVKLSGDTYVSCCVVVKNICRVLYFLPRPIKLSAAVGEDSIPESKRDVYKEVGSLLSNKLGLTE-----FKSK 423 (1429)
T ss_pred ceEEEEeeeeccCCCceEEEEEEcCeeeEEEecccccccccccCCccchhhHHHHHHHHHHHHHhhhhhhH-----hhhh
Confidence 46789998 44589999999998766555 322211 1111122222333333333222110 0111
Q ss_pred EEEeeceeccc----CCceEEEEEEecCcchHHHHHHHHhCCcccCCccceeccCcchhhhhhhhcCCcceeeEEeccee
Q psy5919 156 ICKKFPMYGYH----ADERTFLKILLYEPYHMSKLEDLLLNGAVFNERFQPYESHIPYILQFCIDYNLYGMSNIEFNMVK 231 (387)
Q Consensus 156 ~V~~~~~YGY~----~~~~~FlKI~~~~P~~v~~l~~lL~~g~~~~~~~q~yEahIp~~lrFmiD~nL~G~~wi~~~~~~ 231 (387)
+|++. |-|+ ....+++||.+. ...+++-.-|.. ..-..+|-+|...+=||+++..|-|=.|+++.+..
T Consensus 424 ~v~~~--yafe~~dvp~~~dyLeV~y~--~~~p~LP~Dlkg----dsfshvfgt~tn~lE~fll~rKimGPCWlkv~~~s 495 (1429)
T KOG0970|consen 424 PVKKN--YAFELPDVPMKSDYLEVLYS--YETPKLPSDLKG----DSFSHVFGTNTNPLERFLLSRKIMGPCWLKVKGYS 495 (1429)
T ss_pred hhhhh--hccccCCCCCCCcceEEecc--ccCCCCcccccc----chHHHHhccCccHHHHHHHhccccCceEEEeecCC
Confidence 12221 1222 124678999886 333333222221 11236778899999999999999999999998876
Q ss_pred EEecCCCCCCCCCccceeeEee-cccce
Q psy5919 232 FRSDSETSLPKLSHCQLEADVK-AESIV 258 (387)
Q Consensus 232 ~r~~~~~~~~r~S~C~lEiDv~-~~~Il 258 (387)
.+. ...|+|..|+++. |++|-
T Consensus 496 --~~~----~~~SwCk~Ev~v~sP~nI~ 517 (1429)
T KOG0970|consen 496 --DPP----RNASWCKVEVTVKSPQNIT 517 (1429)
T ss_pred --CCC----CCccceeeEEEecCCcceE
Confidence 332 4689999999986 77776
No 19
>KOG1829|consensus
Probab=85.22 E-value=0.49 Score=50.42 Aligned_cols=57 Identities=23% Similarity=0.240 Sum_probs=51.4
Q ss_pred CCCCCcccCcceeeeccchhhhhhhhhHHHHHHHHhhhhHHHHHhhhcCCCccccCC
Q psy5919 292 GQEPHLLMDPDVYSMQDLLDVKSGALYLKLKDLVSACSIFRMRAILLGQEPHLLMDP 348 (387)
Q Consensus 292 ~~~~~~~~~~~Lys~~d~~~~r~~l~~~~lk~~l~tCr~~~~~~~~~~~~~hl~~~~ 348 (387)
..+.|+++.+++||+.||.+++.+.+...|+++++.-..|+..|.+|..++++|+--
T Consensus 461 ~~~~yL~e~~~~~Sl~DL~~i~~g~L~~~l~~~~k~~~~HV~~C~lC~~~gfiCe~C 517 (580)
T KOG1829|consen 461 AVRRYLTESPHLFSLKDLQDIQDGALLRLLNELTKLSSKHVKECDLCTGKGFICELC 517 (580)
T ss_pred hhhhhhccCchhhhhhhHHHhhcccHHHHHHHHHHHhhhhhhhchhhccCeeeeeec
Confidence 356678899999999999999999888899999999999998899999999999854
No 20
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=79.24 E-value=2.1 Score=47.74 Aligned_cols=36 Identities=28% Similarity=0.683 Sum_probs=33.8
Q ss_pred ccCcEEEeeecCCCCceeEEEEeeccceeeeeCCCC
Q psy5919 33 QKVPVIRVFGNNIEGKKTCVFVHGVFPYLYIPFHHE 68 (387)
Q Consensus 33 ~~vpvir~fG~t~~g~~~c~hvhg~~py~~~~~~~~ 68 (387)
...|++|+||.++.|.++++++=++.||||+.++++
T Consensus 6 ~~~~~~~~~~~~~~G~~v~~~~~~~~~~~~~~~~~~ 41 (792)
T COG0417 6 DGFPLVRIFGDTDSGKSVVKLVATFRPYFYVTLDNS 41 (792)
T ss_pred cCceEEEEeeecCCCCEEEEEecCCCCcEEEecCCC
Confidence 358999999999999999999999999999999976
No 21
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=66.58 E-value=1.9 Score=50.13 Aligned_cols=53 Identities=11% Similarity=0.135 Sum_probs=47.8
Q ss_pred ceEEEEEEecCcchHHHHHHHHhCCcccCCccceeccCcchhhhhhhhcCCcceee
Q psy5919 169 ERTFLKILLYEPYHMSKLEDLLLNGAVFNERFQPYESHIPYILQFCIDYNLYGMSN 224 (387)
Q Consensus 169 ~~~FlKI~~~~P~~v~~l~~lL~~g~~~~~~~q~yEahIp~~lrFmiD~nL~G~~w 224 (387)
+..++|+++.+|..++++++.+.. .+...+.+|+.|||..|+|+|..+..|.|
T Consensus 128 ~~~~~k~~~~~~~~v~~~~~~~~~---~~~~~~~~e~di~~~~r~~~d~~~~p~~~ 180 (1172)
T TIGR00592 128 LVSVPKLKFSSPADVPAINDFSNH---HPAVVDIVKKAIPVSTRYLLEKILIPVPL 180 (1172)
T ss_pred cccccccccccccchhhccccccc---cccccccccCCCCccccccccccccCCCC
Confidence 468899999999999999988765 45678999999999999999999999987
No 22
>cd05767 IgC_MHC_II_alpha Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain. IgC_MHC_II_alpha: Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. In both humans and in mice these molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), for example on B-lymphocytes, monocytes, and macrophages. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from protelytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosom
Probab=63.10 E-value=8.5 Score=31.13 Aligned_cols=24 Identities=29% Similarity=0.505 Sum_probs=19.9
Q ss_pred cEEEeeecCCCC----ceeEEEEeeccc
Q psy5919 36 PVIRVFGNNIEG----KKTCVFVHGVFP 59 (387)
Q Consensus 36 pvir~fG~t~~g----~~~c~hvhg~~p 59 (387)
|.++||...+.+ .+.-||+-||||
T Consensus 2 P~V~v~~~~~~~~~~~~tL~C~a~gFyP 29 (94)
T cd05767 2 PEVTVFSLKPVELGEPNTLICFVDNFFP 29 (94)
T ss_pred CEEEEEeCCcccCCCCeEEEEEEEEEEC
Confidence 778888886654 479999999999
No 23
>cd05767 IgC_MHC_II_alpha Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain. IgC_MHC_II_alpha: Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. In both humans and in mice these molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), for example on B-lymphocytes, monocytes, and macrophages. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from protelytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosom
Probab=49.83 E-value=22 Score=28.72 Aligned_cols=24 Identities=29% Similarity=0.516 Sum_probs=19.3
Q ss_pred cEEEEEEecCCC----CEEEEEEceeee
Q psy5919 88 PVIRVFGNNVEG----KKTCVFVHGVFP 111 (387)
Q Consensus 88 pvIrlFG~T~~G----~svcv~Vhgf~P 111 (387)
|.+++|...+.+ .+..|++.||+|
T Consensus 2 P~V~v~~~~~~~~~~~~tL~C~a~gFyP 29 (94)
T cd05767 2 PEVTVFSLKPVELGEPNTLICFVDNFFP 29 (94)
T ss_pred CEEEEEeCCcccCCCCeEEEEEEEEEEC
Confidence 778889886544 389999999976
No 24
>cd05770 IgC_beta2m Class I major histocompatibility complex (MHC) beta2-microglobulin. IgC_beta2m: Immunoglobulin-like domain in beta2-Microglobulin (beta2m). Beta2m is the non-covalently bound light chain of the human class I major histocompatibility complex (MHC-I). Beta2m is structured as a beta-sandwich domain composed of two facing beta-sheets (four stranded and three stranded), that is typical of the C-type immunoglobulin superfamily. This structure is stabilized by an intramolecular disulfide bridge connecting two Cys residues in the facing beta -sheets. In vivo, MHC-I continuously exposes beta2m on the cell surface, where it may be released to plasmatic fluids, transported to the kidneys, degraded and then excreted.
Probab=46.08 E-value=24 Score=28.40 Aligned_cols=25 Identities=28% Similarity=0.511 Sum_probs=18.7
Q ss_pred cEEEeeecCCC--Cc--eeEEEEeeccce
Q psy5919 36 PVIRVFGNNIE--GK--KTCVFVHGVFPY 60 (387)
Q Consensus 36 pvir~fG~t~~--g~--~~c~hvhg~~py 60 (387)
|.++||-..+. |+ ..-||+-||+|-
T Consensus 2 P~v~v~~~~~~~~g~~~~L~C~a~gFyP~ 30 (93)
T cd05770 2 PKVQVYSRFPAENGKPNVLNCYVTGFHPP 30 (93)
T ss_pred CEEEEEecCCCcCCCceEEEEEEEEEeCC
Confidence 67788865443 44 689999999993
No 25
>cd05766 IgC_MHC_II_beta Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain. IgC_MHC_II_beta: Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II beta chain. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. In both humans and in mice these molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), for example on B-lymphocytes, monocytes, and macrophages. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from protelytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome be
Probab=38.73 E-value=37 Score=27.19 Aligned_cols=24 Identities=17% Similarity=0.401 Sum_probs=17.4
Q ss_pred cEEEeeecCCC----CceeEEEEeeccc
Q psy5919 36 PVIRVFGNNIE----GKKTCVFVHGVFP 59 (387)
Q Consensus 36 pvir~fG~t~~----g~~~c~hvhg~~p 59 (387)
|.+++|...+. -...-|||.||+|
T Consensus 1 p~v~v~~~~~~~~~~~~~L~C~~~gFyP 28 (94)
T cd05766 1 PSVKISPSQTGSLSHPHLLVCHVWGFYP 28 (94)
T ss_pred CEEEEEeCCCccCCCCeEEEEEEeeecC
Confidence 56667765443 1478899999999
No 26
>cd05770 IgC_beta2m Class I major histocompatibility complex (MHC) beta2-microglobulin. IgC_beta2m: Immunoglobulin-like domain in beta2-Microglobulin (beta2m). Beta2m is the non-covalently bound light chain of the human class I major histocompatibility complex (MHC-I). Beta2m is structured as a beta-sandwich domain composed of two facing beta-sheets (four stranded and three stranded), that is typical of the C-type immunoglobulin superfamily. This structure is stabilized by an intramolecular disulfide bridge connecting two Cys residues in the facing beta -sheets. In vivo, MHC-I continuously exposes beta2m on the cell surface, where it may be released to plasmatic fluids, transported to the kidneys, degraded and then excreted.
Probab=34.82 E-value=54 Score=26.41 Aligned_cols=25 Identities=28% Similarity=0.522 Sum_probs=18.6
Q ss_pred cEEEEEEecCC--CC--EEEEEEceeeeE
Q psy5919 88 PVIRVFGNNVE--GK--KTCVFVHGVFPY 112 (387)
Q Consensus 88 pvIrlFG~T~~--G~--svcv~Vhgf~PY 112 (387)
|.+++|-+.+. |+ ...|++.||+|-
T Consensus 2 P~v~v~~~~~~~~g~~~~L~C~a~gFyP~ 30 (93)
T cd05770 2 PKVQVYSRFPAENGKPNVLNCYVTGFHPP 30 (93)
T ss_pred CEEEEEecCCCcCCCceEEEEEEEEEeCC
Confidence 67888876543 44 689999999764
No 27
>PRK05761 DNA polymerase I; Reviewed
Probab=34.06 E-value=36 Score=38.14 Aligned_cols=37 Identities=16% Similarity=0.308 Sum_probs=27.4
Q ss_pred cccCcEEEeeecCCCCceeEEE-EeeccceeeeeCCCCC
Q psy5919 32 IQKVPVIRVFGNNIEGKKTCVF-VHGVFPYLYIPFHHEP 69 (387)
Q Consensus 32 ~~~vpvir~fG~t~~g~~~c~h-vhg~~py~~~~~~~~~ 69 (387)
....||||+||.. +|..+..+ =.|+-||||+..+++.
T Consensus 29 ~~~~~vi~l~~~~-~~~~~~~~d~~gfkPYfy~~~~~~~ 66 (787)
T PRK05761 29 KLGKAVVKLYDPE-TGKIYKWYDRTGHKPYFLTDLDPDE 66 (787)
T ss_pred cCCeeEEEEEecC-CCeEEEEEcCCCCCCeEEecCChHH
Confidence 3467999999996 55544443 3579999999987654
No 28
>TIGR00778 ahpD_dom alkylhydroperoxidase AhpD family core domain. Members of the family include the alkylhydroperoxidase AhpD of Mycobacterium tuberculosis, a macrophage infectivity potentiator peptide of Legionella pneumophila, and an uncharacterized peptide in the tetrachloroethene reductive dehalogenase operon of Dehalospirillum multivorans. We suggest that many peptides containing this domain may have alkylhydroperoxidase or related antioxidant activity.
Probab=31.71 E-value=21 Score=24.67 Aligned_cols=25 Identities=28% Similarity=0.397 Sum_probs=22.7
Q ss_pred cccHHHHHHHHHHhhccccccccCC
Q psy5919 362 GALYLKLKDLVSACSSHVYNCEPTN 386 (387)
Q Consensus 362 G~l~~~l~~l~~~~~~Hv~~C~lC~ 386 (387)
|.|-+..++|+........+|.-|.
T Consensus 1 g~l~~~~reli~l~~s~~~~C~yc~ 25 (50)
T TIGR00778 1 GALDAATKELIAIAVSQINGCGYCL 25 (50)
T ss_pred CCCCHHHHHHHHHHHHHHcCCHHHH
Confidence 5688999999999999999999885
No 29
>cd07698 IgC_MHC_I_alpha3 Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain. IgC_MHC_I_alpha3; Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I alpha chain. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta2 microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.
Probab=29.75 E-value=61 Score=25.55 Aligned_cols=25 Identities=20% Similarity=0.371 Sum_probs=18.9
Q ss_pred cEEEeeecCC--CCceeEEEEeeccce
Q psy5919 36 PVIRVFGNNI--EGKKTCVFVHGVFPY 60 (387)
Q Consensus 36 pvir~fG~t~--~g~~~c~hvhg~~py 60 (387)
|.+.+|.... .....-|++.||+|=
T Consensus 3 P~v~v~~~~~~~~~~~L~C~a~gF~P~ 29 (93)
T cd07698 3 PEVRVTRKRAPDGSLTLSCHATGFYPR 29 (93)
T ss_pred CEEEEEecCCCCCcEEEEEEEEEEeCC
Confidence 6677777764 346789999999993
No 30
>cd07698 IgC_MHC_I_alpha3 Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain. IgC_MHC_I_alpha3; Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I alpha chain. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta2 microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.
Probab=21.40 E-value=1.2e+02 Score=23.84 Aligned_cols=26 Identities=19% Similarity=0.349 Sum_probs=19.8
Q ss_pred ccEEEEEEecCC--CCEEEEEEceeeeE
Q psy5919 87 VPVIRVFGNNVE--GKKTCVFVHGVFPY 112 (387)
Q Consensus 87 ~pvIrlFG~T~~--G~svcv~Vhgf~PY 112 (387)
.|.+.+|..... ....-|++.||+|=
T Consensus 2 pP~v~v~~~~~~~~~~~L~C~a~gF~P~ 29 (93)
T cd07698 2 PPEVRVTRKRAPDGSLTLSCHATGFYPR 29 (93)
T ss_pred CCEEEEEecCCCCCcEEEEEEEEEEeCC
Confidence 477888888743 35888999999764
No 31
>cd05772 IgC_SIRP Signal-regulatory protein (SIRP) immunoglobulin-like domain. IgC_SIRP: Immunoglobulin-like domain of signal-regulatory proteins (SIRP); the signal-regulatory proteins (SIRP) are Ig-like cell surface receptors detected in hematopoietic and non-hematopoietic cells. While their extracellular domains are similar, SIRP are classified as alpha or beta based on the length of the intracytoplasmic domain. Those having a 110- to 113-amino acid tail are classified as SIRP-alpha, and those having a 5-amino acid tail as SIRP-beta. SIRP-alpha and SIRP-beta molecules are thought to have complementary roles in signal regulation: SIRP-alpha inhibit signalling via their immunoreceptor tyrosine (IT)-based inhibition motifs while SIRP-beta are activating. SIRP-beta lack the cytoplasmic domainof SIRP-alpha, and associate with at least one other transmembrane protein (DAP-12 or KARAP). The IT-based activation motifs within DAP-12's cytoplasmic domain may link SIRP-beta to the activating
Probab=21.03 E-value=81 Score=26.19 Aligned_cols=27 Identities=26% Similarity=0.319 Sum_probs=20.0
Q ss_pred ccCcEEEeeecC-CCC--ceeEEEEeeccc
Q psy5919 33 QKVPVIRVFGNN-IEG--KKTCVFVHGVFP 59 (387)
Q Consensus 33 ~~vpvir~fG~t-~~g--~~~c~hvhg~~p 59 (387)
..+|+|..+-.. ..| .+.-||+.||+|
T Consensus 6 P~~p~i~~~~~~~~~g~~~tL~C~a~gF~P 35 (111)
T cd05772 6 PSVPVVSGPSGRANPGQSVNFTCSAHGFSP 35 (111)
T ss_pred CCCcEeCCchhccCCCCCEEEEEEEeeEeC
Confidence 367888876442 234 488999999999
Done!