BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 042238
(459 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2BGH|A Chain A, Crystal Structure Of Vinorine Synthase
pdb|2BGH|B Chain B, Crystal Structure Of Vinorine Synthase
Length = 421
Score = 213 bits (541), Expect = 2e-55, Method: Compositional matrix adjust.
Identities = 150/434 (34%), Positives = 218/434 (50%), Gaps = 38/434 (8%)
Query: 4 ALEVEIVAKEAIKPSYPTPHYLRNFKRSLMDQINYPMYTTGIFIYKVNDDDDLSVKAGRI 63
A ++E V++E I PS PTP L+ +K S +DQ+ + I Y D +L +
Sbjct: 2 APQMEKVSEELILPSSPTPQSLKCYKISHLDQLLLTCHIPFILFYPNPLDSNLD--PAQT 59
Query: 64 SRRLKSSLSETLTKFYPFAGKVKDDFSIECNDDGVEFIEGRANGFLSQYLQ------EPD 117
S+ LK SLS+ LT FYP AG++ + S++CND GV F+E R LSQ +Q + D
Sbjct: 60 SQHLKQSLSKVLTHFYPLAGRINVNSSVDCNDSGVPFVEARVQAQLSQAIQNVVELEKLD 119
Query: 118 HNLLSEFHPFGKEGPVAGKDSPLLIVQATFFKCGGVAIATCASHVLIDGMSLATFINCWA 177
L S +P GK +D P L V+ +FF+CGG AI SH + D +SLATF+N W
Sbjct: 120 QYLPSAAYPGGKIE--VNEDVP-LAVKISFFECGGTAIGVNLSHKIADVLSLATFLNAWT 176
Query: 178 ATARVDDHHQPSKLPASMLPQY-VTASLFPASEAVSSYPLRFSPSERVEFNRFVFDASKI 236
AT R + +LP + + A FP + S L P E V RFVFD KI
Sbjct: 177 ATCRGETE--------IVLPNFDLAARHFPPVDNTPSPEL--VPDENVVMKRFVFDKEKI 226
Query: 237 AQLKAEAASEIVPRP-STVEAITALIWKCTRTASRSNHGGSPRPSLLLQGANFRTELVPP 295
L+A+A+S + S V+ + A IWK +R+ +G + +++Q N R+ + PP
Sbjct: 227 GALRAQASSASEEKNFSRVQLVVAYIWKHVIDVTRAKYGAKNK-FVVVQAVNLRSRMNPP 285
Query: 296 LPDNSVGNCVGYAVAQT-GEKETKLQDLVCELRRAKEEFSRNGLQTLLEN-KCLLTIQDQ 353
LP ++GN A E + DL+ LR + E+ + LL+ CL ++ Q
Sbjct: 286 LPHYAMGNIATLLFAAVDAEWDKDFPDLIGPLRTSLEKTEDDHNHELLKGMTCLYELEPQ 345
Query: 354 SIRDKFESGEIDFFSFTSVVRFPFYQAADFGWGKPIHVTFLNFVSPNFFMLMATNDGTGV 413
+ SFTS R FY DFGWGKP+ F N +LM T G GV
Sbjct: 346 -----------ELLSFTSWCRLGFYD-LDFGWGKPLSACTTTFPKRNAALLMDTRSGDGV 393
Query: 414 EALVSLSPEDMVLF 427
EA + ++ ++M +
Sbjct: 394 EAWLPMAEDEMAML 407
>pdb|4G0B|A Chain A, Structure Of Native Hct From Coffea Canephora
pdb|4G0B|B Chain B, Structure Of Native Hct From Coffea Canephora
Length = 436
Score = 115 bits (289), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 117/450 (26%), Positives = 193/450 (42%), Gaps = 46/450 (10%)
Query: 4 ALEVEIVAKEAIKPSYPTPHYLRNFKRSLMDQINYPMYTTGIFIYKVNDDDDLSVKAGRI 63
A+++E+ ++P+ TP RN S +D + +T ++ Y+ +
Sbjct: 2 AMKIEVKESTMVRPAQETPG--RNLWNSNVDLVVPNFHTPSVYFYRPTGSSNFF-----D 54
Query: 64 SRRLKSSLSETLTKFYPFAGKVKDD----FSIECNDDGVEFIEGRANGFLSQYLQEPDHN 119
++ LK +LS L FYP AG++K D IECN +GV F+E ++G + +
Sbjct: 55 AKVLKDALSRALVPFYPMAGRLKRDEDGRIEIECNGEGVLFVEAESDGVVDDFGDFAPTL 114
Query: 120 LLSEFHPFGKEGPVAGKDSPLLIVQATFFKCGGVAIATCASHVLIDGMSLATFINCWAAT 179
L P + LL++Q T+FKCGGV++ H DG S FIN W+
Sbjct: 115 ELRRLIP-AVDYSQGISSYALLVLQVTYFKCGGVSLGVGMRHHAADGFSGLHFINSWSDM 173
Query: 180 ARVDDHHQPSKLPASML-------PQYVTASLF-PASEAVSSYPLRFSPSERVEFNRFVF 231
AR D P + ++L PQ+ P + VS + + F
Sbjct: 174 ARGLDVTLPPFIDRTLLRARDPPQPQFQHIEYQPPPALKVSPQTAKSDSVPETAVSIFKL 233
Query: 232 DASKIAQLKAEAASEI-VPRPSTVEAITALIWKCTRTASRSNHGGSPRPSLLLQGANFRT 290
+I+ LKA++ + S+ E + +W+C A ++ + + L + R
Sbjct: 234 TREQISALKAKSKEDGNTISYSSYEMLAGHVWRC---ACKARGLEVDQGTKLYIATDGRA 290
Query: 291 ELVPPLPDNSVGNCVGYA--VAQTGEKE--------TKLQDLVCELRRAKEEFSRNGLQT 340
L P LP GN + A +A G+ E +K+ D L R ++ R+ L
Sbjct: 291 RLRPSLPPGYFGNVIFTATPIAIAGDLEFKPVWYAASKIHD---ALARMDNDYLRSALDY 347
Query: 341 LLENKCLLTIQDQSIRDKFESGEIDFFSFTSVVRFPFYQAADFGWGKPIHV--TFLNFVS 398
L L +++ + + TS VR P + ADFGWG+PI + + +
Sbjct: 348 LELQPDL-----KALVRGAHTFKCPNLGITSWVRLPIHD-ADFGWGRPIFMGPGGIAYEG 401
Query: 399 PNFFMLMATNDGTGVEALVSLSPEDMVLFQ 428
+F + TNDG+ + +SL E M LFQ
Sbjct: 402 LSFILPSPTNDGS-MSVAISLQGEHMKLFQ 430
>pdb|4G2M|A Chain A, Structure Of A Lys-Hct Mutant From Coffea Canephora
(Crystal Form 2)
Length = 439
Score = 115 bits (288), Expect = 6e-26, Method: Compositional matrix adjust.
Identities = 118/450 (26%), Positives = 192/450 (42%), Gaps = 46/450 (10%)
Query: 4 ALEVEIVAKEAIKPSYPTPHYLRNFKRSLMDQINYPMYTTGIFIYKVNDDDDLSVKAGRI 63
++++E+ ++P+ TP RN S +D + +T ++ Y+ +
Sbjct: 5 SMKIEVKESTMVRPAQETPG--RNLWNSNVDLVVPNFHTPSVYFYRPTGSSNFF-----D 57
Query: 64 SRRLKSSLSETLTKFYPFAGKVKDD----FSIECNDDGVEFIEGRANGFLSQYLQEPDHN 119
++ LK +LS L FYP AG++K D IECN +GV F+E ++G + +
Sbjct: 58 AKVLKDALSRALVPFYPMAGRLKRDEDGRIEIECNGEGVLFVEAESDGVVDDFGDFAPTL 117
Query: 120 LLSEFHPFGKEGPVAGKDSPLLIVQATFFKCGGVAIATCASHVLIDGMSLATFINCWAAT 179
L P + LL++Q T+FKCGGV++ H DG S FIN W+
Sbjct: 118 ELRRLIP-AVDYSQGISSYALLVLQVTYFKCGGVSLGVGMRHHAADGFSGLHFINSWSDM 176
Query: 180 ARVDDHHQPSKLPASML-------PQYVTASLF-PASEAVSSYPLRFSPSERVEFNRFVF 231
AR D P + ++L PQ+ P + AVS + F
Sbjct: 177 ARGLDVTLPPFIDRTLLRARDPPQPQFQHIEYQPPPALAVSPQTAASDSVPETAVSIFKL 236
Query: 232 DASKIAQLKAEAASEI-VPRPSTVEAITALIWKCTRTASRSNHGGSPRPSLLLQGANFRT 290
+I+ LKA++ + S+ E + +W+C A ++ + + L + R
Sbjct: 237 TREQISALKAKSKEDGNTISYSSYEMLAGHVWRC---ACKARGLEVDQGTKLYIATDGRA 293
Query: 291 ELVPPLPDNSVGNCVGYA--VAQTGEKE--------TKLQDLVCELRRAKEEFSRNGLQT 340
L P LP GN + A +A G+ E +K+ D L R ++ R+ L
Sbjct: 294 RLRPSLPPGYFGNVIFTATPIAIAGDLEFKPVWYAASKIHD---ALARMDNDYLRSALDY 350
Query: 341 LLENKCLLTIQDQSIRDKFESGEIDFFSFTSVVRFPFYQAADFGWGKPIHV--TFLNFVS 398
L L + + K + TS VR P + ADFGWG+PI + + +
Sbjct: 351 LELQPDLKALVRGAHTFKXPN-----LGITSWVRLPIHD-ADFGWGRPIFMGPGGIAYEG 404
Query: 399 PNFFMLMATNDGTGVEALVSLSPEDMVLFQ 428
+F + TNDG+ + +SL E M LFQ
Sbjct: 405 LSFILPSPTNDGS-MSVAISLQGEHMKLFQ 433
>pdb|4G22|A Chain A, Structure Of A Lys-Hct Mutant From Coffea Canephora
(Crystal Form 1)
pdb|4G22|B Chain B, Structure Of A Lys-Hct Mutant From Coffea Canephora
(Crystal Form 1)
Length = 439
Score = 110 bits (276), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 117/450 (26%), Positives = 191/450 (42%), Gaps = 46/450 (10%)
Query: 4 ALEVEIVAKEAIKPSYPTPHYLRNFKRSLMDQINYPMYTTGIFIYKVNDDDDLSVKAGRI 63
++++E+ ++P+ TP RN S +D + +T ++ Y+ +
Sbjct: 5 SMKIEVKESTMVRPAQETPG--RNLWNSNVDLVVPNFHTPSVYFYRPTGSSNFF-----D 57
Query: 64 SRRLKSSLSETLTKFYPFAGKVKDD----FSIECNDDGVEFIEGRANGFLSQYLQEPDHN 119
++ LK +LS L FYP AG++K D IECN +GV F+E ++G + +
Sbjct: 58 AKVLKDALSRALVPFYPMAGRLKRDEDGRIEIECNGEGVLFVEAESDGVVDDFGDFAPTL 117
Query: 120 LLSEFHPFGKEGPVAGKDSPLLIVQATFFKCGGVAIATCASHVLIDGMSLATFINCWAAT 179
L P + LL++Q T+FK GGV++ H DG S FIN W+
Sbjct: 118 ELRRLIP-AVDYSQGISSYALLVLQVTYFKXGGVSLGVGMRHHAADGFSGLHFINSWSDM 176
Query: 180 ARVDDHHQPSKLPASML-------PQYVTASLF-PASEAVSSYPLRFSPSERVEFNRFVF 231
AR D P + ++L PQ+ P + AVS + F
Sbjct: 177 ARGLDVTLPPFIDRTLLRARDPPQPQFQHIEYQPPPALAVSPQTAASDSVPETAVSIFKL 236
Query: 232 DASKIAQLKAEAASEI-VPRPSTVEAITALIWKCTRTASRSNHGGSPRPSLLLQGANFRT 290
+I+ LKA++ + S+ E + +W+C A ++ + + L + R
Sbjct: 237 TREQISALKAKSKEDGNTISYSSYEMLAGHVWRC---ACKARGLEVDQGTKLYIATDGRA 293
Query: 291 ELVPPLPDNSVGNCVGYA--VAQTGEKE--------TKLQDLVCELRRAKEEFSRNGLQT 340
L P LP GN + A +A G+ E +K+ D L R ++ R+ L
Sbjct: 294 RLRPSLPPGYFGNVIFTATPIAIAGDLEFKPVWYAASKIHD---ALARMDNDYLRSALDY 350
Query: 341 LLENKCLLTIQDQSIRDKFESGEIDFFSFTSVVRFPFYQAADFGWGKPIHV--TFLNFVS 398
L L + + K + TS VR P + ADFGWG+PI + + +
Sbjct: 351 LELQPDLKALVRGAHTFKXPN-----LGITSWVRLPIHD-ADFGWGRPIFMGPGGIAYEG 404
Query: 399 PNFFMLMATNDGTGVEALVSLSPEDMVLFQ 428
+F + TNDG+ + +SL E M LFQ
Sbjct: 405 LSFILPSPTNDGS-MSVAISLQGEHMKLFQ 433
>pdb|2E1T|A Chain A, Crystal Structure Of Dendranthema Morifolium Dmat
Complexed With Malonyl-coa
pdb|2E1T|B Chain B, Crystal Structure Of Dendranthema Morifolium Dmat
Complexed With Malonyl-coa
pdb|2E1U|A Chain A, Crystal Structure Of Dendranthema Morifolium Dmat
pdb|2E1U|B Chain B, Crystal Structure Of Dendranthema Morifolium Dmat
Length = 454
Score = 68.2 bits (165), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 100/367 (27%), Positives = 146/367 (39%), Gaps = 74/367 (20%)
Query: 67 LKSSLSETLTKFYPFAGKVKDDFSIECNDDGVEFIEGR--ANGFLSQYLQEPDHNLLSEF 124
+K SLS TL FYPF GK+ + + ++EG A F L D N L+
Sbjct: 65 IKHSLSITLKHFYPFVGKLVV-YPAPTKKPEICYVEGDSVAVTFAECNL---DLNELTGN 120
Query: 125 HP-----FGKEGPVAGKDS--------PLLIVQATFFKCGGVAIATCASHVLIDGMSLAT 171
HP F P+ G+ + PL VQ T F G+AI H L D +
Sbjct: 121 HPRNCDKFYDLVPILGESTRLSDCIKIPLFSVQVTLFPNQGIAIGITNHHCLGDASTRFC 180
Query: 172 FINCWAATARVDDHHQPSKLPASMLPQYVTASLFPASE-------AVSSYPLRF------ 218
F+ W + AR ++ + S L P Y +P + V S+ +
Sbjct: 181 FLKAWTSIARSGNNDE-SFLANGTRPLYDRIIKYPMLDEAYLKRAKVESFNEDYVTQSLA 239
Query: 219 SPSERVEFNRFVFDASKIAQLKAEAASEIVPRPSTVEAIT---ALIWKCTRTASRSNHGG 275
PS+++ F+ + I QLK +++ P V + T A IW C SR++
Sbjct: 240 GPSDKLR-ATFILTRAVINQLKDRVLAQL-PTLEYVSSFTVACAYIWSCI-AKSRND--- 293
Query: 276 SPRPSLLLQGANFRTELVPPLPDNSVGNCVG--YAVAQTGEKETKLQDLVCELRRAKEEF 333
+ L + R + PP+P GNCVG A+A+T L KE F
Sbjct: 294 --KLQLFGFPIDRRARMKPPIPTAYFGNCVGGCAAIAKT------------NLLIGKEGF 339
Query: 334 SRNGLQTLLEN--KCLLTIQDQSIRDKFES----------GEIDFFSFTSVVRFPFYQAA 381
+ + EN K L +D ++D ES + + S T +RF
Sbjct: 340 I-TAAKLIGENLHKTLTDYKDGVLKDDMESFNDLVSEGMPTTMTWVSGTPKLRF---YDM 395
Query: 382 DFGWGKP 388
DFGWGKP
Sbjct: 396 DFGWGKP 402
>pdb|2E1V|A Chain A, Crystal Structure Of Dendranthema Morifolium Dmat, Seleno-
Methionine Derivative
pdb|2E1V|B Chain B, Crystal Structure Of Dendranthema Morifolium Dmat, Seleno-
Methionine Derivative
Length = 454
Score = 65.5 bits (158), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 100/367 (27%), Positives = 144/367 (39%), Gaps = 74/367 (20%)
Query: 67 LKSSLSETLTKFYPFAGKVKDDFSIECNDDGVEFIEGR--ANGFLSQYLQEPDHNLLSEF 124
+K SLS TL FYPF GK+ + + ++EG A F L D N L+
Sbjct: 65 IKHSLSITLKHFYPFVGKLVV-YPAPTKKPEICYVEGDSVAVTFAECNL---DLNELTGN 120
Query: 125 HP-----FGKEGPVAGKDS--------PLLIVQATFFKCGGVAIATCASHVLIDGMSLAT 171
HP F P+ G+ + PL VQ T F G+AI H L D +
Sbjct: 121 HPRNCDKFYDLVPILGESTRLSDCIKIPLFSVQVTLFPNQGIAIGITNHHCLGDASTRFC 180
Query: 172 FINCWAATARVDDHHQPSKLPASMLPQYVTASLFPASE-------AVSSYPLRF------ 218
F+ W + AR ++ + S L P Y +P + V S+ +
Sbjct: 181 FLKAWTSIARSGNNDE-SFLANGTRPLYDRIIKYPXLDEAYLKRAKVESFNEDYVTQSLA 239
Query: 219 SPSERVEFNRFVFDASKIAQLKAEAASEIVPRPSTVEAIT---ALIWKCTRTASRSNHGG 275
PS+++ F+ + I QLK +++ P V + T A IW C SR++
Sbjct: 240 GPSDKLR-ATFILTRAVINQLKDRVLAQL-PTLEYVSSFTVACAYIWSCI-AKSRND--- 293
Query: 276 SPRPSLLLQGANFRTELVPPLPDNSVGNCVG--YAVAQTGEKETKLQDLVCELRRAKEEF 333
+ L + R PP+P GNCVG A+A+T L KE F
Sbjct: 294 --KLQLFGFPIDRRARXKPPIPTAYFGNCVGGCAAIAKT------------NLLIGKEGF 339
Query: 334 SRNGLQTLLEN--KCLLTIQDQSIRDKFES----------GEIDFFSFTSVVRFPFYQAA 381
+ + EN K L +D ++D ES + S T +RF
Sbjct: 340 I-TAAKLIGENLHKTLTDYKDGVLKDDXESFNDLVSEGXPTTXTWVSGTPKLRF---YDX 395
Query: 382 DFGWGKP 388
DFGWGKP
Sbjct: 396 DFGWGKP 402
>pdb|2XR7|A Chain A, Crystal Structure Of Nicotiana Tabacum Malonyltransferase
(Ntmat1) Complexed With Malonyl-Coa
Length = 453
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 90/376 (23%), Positives = 141/376 (37%), Gaps = 75/376 (19%)
Query: 67 LKSSLSETLTKFYPFAGKVKDDFSIECNDDGVEFIEGR--ANGFLSQYLQEPDH--NLLS 122
LK SLS TL + P AG V C D + E R +S E D N L
Sbjct: 60 LKDSLSLTLKYYLPLAGNVA------CPQDWSGYPELRYVTGNSVSVIFSESDXDFNYLI 113
Query: 123 EFHPFG--------------KEGPVAGKDSPLLIVQATFFKCGGVAIATCASHVLIDGMS 168
+HP K+ P + +P+L +Q T F G++I HV DG +
Sbjct: 114 GYHPRNTKDFYHFVPQLAEPKDAP-GVQLAPVLAIQVTLFPNHGISIGFTNHHVAGDGAT 172
Query: 169 LATFINCWAATARVDDHHQPSKLPASMLPQY----------VTASLFPASEAVSSYPLR- 217
+ F+ WA + Q L +P Y V S++ +
Sbjct: 173 IVKFVRAWALLNKFGGDEQ--FLANEFIPFYDRSVIKDPNGVGXSIWNEXKKYKHXXKXS 230
Query: 218 --FSPSERVEFNRFVFDASKIAQLKAEAASEIVPRPSTVEAIT---ALIWKC-----TRT 267
+P ++V F+ I +LK + P+ + V + T A +W C T
Sbjct: 231 DVVTPPDKVR-GTFIITRHDIGKLKNLVLTR-RPKLTHVTSFTVTCAYVWTCIIKSEAAT 288
Query: 268 ASRSNHGGSPRPSLLLQGANFRTELVPPLPDNSVGNC-VGYAVAQTGEKE-------TKL 319
+ G A+ R + PPLP + GN VGY VA+T + + T
Sbjct: 289 GEEIDENGX---EFFGCAADCRAQFNPPLPPSYFGNALVGY-VARTRQVDLAGKEGFTIA 344
Query: 320 QDLVCELRRAKEEFSRNGLQTLLENKCLLTIQDQSIRDKFESGEIDFFSFTSVVRFPFYQ 379
+L+ E R + + + + +L+ DK ++ S + Y
Sbjct: 345 VELIGEAIRKRXK----------DEEWILSGSWFKEYDKVDAKRS--LSVAGSPKLDLY- 391
Query: 380 AADFGWGKPIHVTFLN 395
AADFGWG+P + F++
Sbjct: 392 AADFGWGRPEKLEFVS 407
>pdb|1NT9|G Chain G, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|G Chain G, Rna Polymerase Ii-Tfiis Complex
pdb|1WCM|G Chain G, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|G Chain G, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|G Chain G, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|G Chain G, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|G Chain G, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|1Y14|B Chain B, Crystal Structure Of Yeast Subcomplex Of Rpb4 And Rpb7
pdb|1Y14|D Chain D, Crystal Structure Of Yeast Subcomplex Of Rpb4 And Rpb7
pdb|2B63|G Chain G, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2JA5|G Chain G, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|G Chain G, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|G Chain G, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|S Chain S, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|G Chain G, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2R7Z|G Chain G, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|G Chain G, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|G Chain G, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|G Chain G, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3FKI|G Chain G, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3H3V|H Chain H, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|G Chain G, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|S Chain S, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|G Chain G, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|G Chain G, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|G Chain G, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|G Chain G, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|G Chain G, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|G Chain G, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|G Chain G, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|G Chain G, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3PO2|G Chain G, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|G Chain G, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|G Chain G, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3J0K|G Chain G, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
pdb|4A3C|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|G Chain G, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|G Chain G, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
pdb|4BBR|G Chain G, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|G Chain G, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 171
Score = 35.8 bits (81), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 25/107 (23%), Positives = 47/107 (43%), Gaps = 3/107 (2%)
Query: 14 AIKPSYPTPHYLRNFKRSLMDQINYPMYTTGIFIYKVNDDDDLSVKAGRI---SRRLKSS 70
+ PS+ P + K L++++ +I V D D++ ++ GRI + +
Sbjct: 12 TLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFN 71
Query: 71 LSETLTKFYPFAGKVKDDFSIECNDDGVEFIEGRANGFLSQYLQEPD 117
+ F PF G+V D + C+ G E G F++++L D
Sbjct: 72 VKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQD 118
>pdb|2B8K|G Chain G, 12-Subunit Rna Polymerase Ii
Length = 215
Score = 35.4 bits (80), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 25/107 (23%), Positives = 47/107 (43%), Gaps = 3/107 (2%)
Query: 14 AIKPSYPTPHYLRNFKRSLMDQINYPMYTTGIFIYKVNDDDDLSVKAGRI---SRRLKSS 70
+ PS+ P + K L++++ +I V D D++ ++ GRI + +
Sbjct: 12 TLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFN 71
Query: 71 LSETLTKFYPFAGKVKDDFSIECNDDGVEFIEGRANGFLSQYLQEPD 117
+ F PF G+V D + C+ G E G F++++L D
Sbjct: 72 VKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQD 118
>pdb|2ZUK|A Chain A, The Crystal Structure Of Alpha-Amino-Epsilon-Caprolactam
Racemase From Achromobacter Obae Complexed With Epsilon
Caprolactam (Different Binding Mode)
pdb|2ZUK|B Chain B, The Crystal Structure Of Alpha-Amino-Epsilon-Caprolactam
Racemase From Achromobacter Obae Complexed With Epsilon
Caprolactam (Different Binding Mode)
pdb|3DXV|A Chain A, The Crystal Structure Of Alpha-Amino-Epsilon-Caprolactam
Racemase From Achromobacter Obae
pdb|3DXV|B Chain B, The Crystal Structure Of Alpha-Amino-Epsilon-Caprolactam
Racemase From Achromobacter Obae
Length = 439
Score = 30.0 bits (66), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 42 TTGIFIYKVNDDDDLSVKAGRISRRLKSSLSETLTKFYPFAGKVK 86
G+ + + D DDL A R R L+ LSE L K +P G ++
Sbjct: 307 AAGLAVLETIDRDDLPAMAERKGRLLRDGLSE-LAKRHPLIGDIR 350
>pdb|3DXW|A Chain A, The Crystal Structure Of Alpha-Amino-Epsilon-Caprolactam
Racemase From Achromobacter Obae Complexed With Epsilon
Caprolactam
pdb|3DXW|B Chain B, The Crystal Structure Of Alpha-Amino-Epsilon-Caprolactam
Racemase From Achromobacter Obae Complexed With Epsilon
Caprolactam
Length = 452
Score = 30.0 bits (66), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 42 TTGIFIYKVNDDDDLSVKAGRISRRLKSSLSETLTKFYPFAGKVK 86
G+ + + D DDL A R R L+ LSE L K +P G ++
Sbjct: 320 AAGLAVLETIDRDDLPAMAERKGRLLRDGLSE-LAKRHPLIGDIR 363
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.319 0.135 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,211,183
Number of Sequences: 62578
Number of extensions: 535956
Number of successful extensions: 1099
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1069
Number of HSP's gapped (non-prelim): 13
length of query: 459
length of database: 14,973,337
effective HSP length: 102
effective length of query: 357
effective length of database: 8,590,381
effective search space: 3066766017
effective search space used: 3066766017
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)