RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 029236
(196 letters)
>1zps_A PRA-CH, phosphoribosyl-AMP cyclohydrolase; histidine biosynthesis;
1.70A {Methanothermobacterthermautotrophicus} SCOP:
b.168.1.1
Length = 138
Score = 143 bits (362), Expect = 2e-44
Identities = 37/100 (37%), Positives = 63/100 (63%)
Query: 56 SVKWDNKGLAVAIAQNVDTGAILMQGFANRDALATTISSRKATFYSRSRSTLWTKGETSQ 115
+ + L +A+AQ+ +TG +LM + NR+AL T+ + A ++S SR LW KGE+S
Sbjct: 15 RHNINGEDLIIAVAQDHETGEVLMVAYMNREALRRTLETGTAHYWSTSRGKLWLKGESSG 74
Query: 116 NFINVQDIFLDCDRDSIIYLGKPDGPTCHTGSETCYYTSV 155
+ V+D+ +DCD D+++ + +G CHTG +C+Y S+
Sbjct: 75 HVQRVKDVLVDCDGDAVVLKVEQEGGACHTGYRSCFYRSI 114
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 38.5 bits (89), Expect = 8e-04
Identities = 15/93 (16%), Positives = 36/93 (38%), Gaps = 6/93 (6%)
Query: 99 FYSRSRS--TLWTKGE--TSQNF-INVQDIFLDCDRDSIIYLGKPDGPTCHTGSETCYYT 153
Y S++ +W + + + ++ DI ++ + I+ G G +
Sbjct: 1635 LYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFE 1694
Query: 154 SVLDA-LKDQPVGSFISLAHTAVLFGIPESELD 185
+++D LK + + I+ T+ F + L
Sbjct: 1695 TIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLS 1727
Score = 33.5 bits (76), Expect = 0.043
Identities = 41/203 (20%), Positives = 62/203 (30%), Gaps = 61/203 (30%)
Query: 9 VQSLKVSLTGSDRCRDNDMKRNCLV---FASSTESNSNPVLQSKVDRLLDSVKWDNKGLA 65
+ +L L + +K L+ + + P + L +V +G A
Sbjct: 101 IHALAAKLLQENDTT--LVKTKELIKNYITARIMAKR-PFDKKSNSALFRAV---GEGNA 154
Query: 66 VAIAQ-NVDTGAILMQGFAN------RDALATTISSRKATFYSRSRSTLW----TKGETS 114
+A G QG + RD L T S TL T +
Sbjct: 155 QLVAIFG---G----QGNTDDYFEELRD-LYQTYHVLVGDLIKFSAETLSELIRTTLDAE 206
Query: 115 QNFINVQDI--FLDCDRDSIIYLGKPDGPTCHTGSETCYYTSVLDALKDQPVGSF----- 167
+ F +I +L+ + + PD Y S+ P+ S
Sbjct: 207 KVFTQGLNILEWLE-NPSN-----TPDKD---------YLLSI-------PI-SCPLIGV 243
Query: 168 ISLAH---TAVLFGIPESELDSS 187
I LAH TA L G EL S
Sbjct: 244 IQLAHYVVTAKLLGFTPGELRSY 266
Score = 28.1 bits (62), Expect = 2.3
Identities = 17/92 (18%), Positives = 35/92 (38%), Gaps = 20/92 (21%)
Query: 10 QSLKV----SLTGSD-RCRDNDMKRN---CLV-----FASSTESNSNPVL------QSKV 50
+ +++ + GSD R + C++ + ++T+ + +L S +
Sbjct: 453 KDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGL 512
Query: 51 DRLLDSVKWDNKGLAVAIAQNVDTGAILMQGF 82
L K D G+ V +A +D GF
Sbjct: 513 GVLTHRNK-DGTGVRVIVAGTLDINPDDDYGF 543
Score = 27.3 bits (60), Expect = 3.8
Identities = 21/118 (17%), Positives = 36/118 (30%), Gaps = 34/118 (28%)
Query: 87 ALATTISSRKATFYSRSRSTL----WTKGETSQNFINVQDIFLDCDRDSI-IYLGKPDGP 141
A+A + +F+ R + + G + DS+ G P
Sbjct: 280 AVAIAETDSWESFFVSVRKAITVLFFI-GVRCYEAYPNTSLPPSILEDSLENNEGVP--- 335
Query: 142 TCHTGSETCYYTSVLDALKDQ------------PVGS--FISLAHTA---VLFGIPES 182
S+ + ++Q P G ISL + A V+ G P+S
Sbjct: 336 --------SPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQS 385
>3lo7_A PBPA, penicillin-binding protein A; transpeptidase domain, cell
membrane, cell shape, cell WALL biogenesis/degradation,
membrane; 2.05A {Mycobacterium tuberculosis}
Length = 483
Score = 31.5 bits (72), Expect = 0.17
Identities = 11/37 (29%), Positives = 15/37 (40%), Gaps = 3/37 (8%)
Query: 43 NPVLQSKVDRLLDSVKW-DNKGLAVAIAQNVDTGAIL 78
NP +Q + + KG VA+ TG IL
Sbjct: 131 NPRIQQAGWDAMQQGCYGPCKGAVVAL--EPSTGKIL 165
>2ycu_A Non muscle myosin 2C, alpha-actinin; motor protein; HET: AOV; 2.25A
{Homo sapiens} PDB: 1br1_A* 1br4_A* 1br2_A*
Length = 995
Score = 30.8 bits (70), Expect = 0.31
Identities = 14/67 (20%), Positives = 19/67 (28%), Gaps = 21/67 (31%)
Query: 66 VAIAQNVDTGAILMQGFANRDALATTISSRKATFYSR------SR--STLWTKGETSQNF 117
V AQ + Q +ALA Y R R L +F
Sbjct: 382 VQKAQTKE------QADFALEALAKAT-------YERLFRWLVLRLNRALDRSPRQGASF 428
Query: 118 INVQDIF 124
+ + DI
Sbjct: 429 LGILDIA 435
>3p9x_A Phosphoribosylglycinamide formyltransferase; structural genomics,
PSI-biology, protein STRU initiative; 1.90A {Bacillus
halodurans}
Length = 211
Score = 29.8 bits (68), Expect = 0.47
Identities = 10/72 (13%), Positives = 27/72 (37%), Gaps = 15/72 (20%)
Query: 27 MKRNCLVFASSTESNSNPVLQSKVDR-----------LLDSVKWDNKGLAVAIAQNVDTG 75
+ + +FAS + +N ++ + LL + K K + +
Sbjct: 1 VMKRVAIFASGSGTN----AEAIIQSQKAGQLPCEVALLITDKPGAKVVERVKVHEIPVC 56
Query: 76 AILMQGFANRDA 87
A+ + + +++A
Sbjct: 57 ALDPKTYPSKEA 68
>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin
subfragment 2, heavy meromyosin, essential light chain,
motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP:
i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A
Length = 1184
Score = 30.2 bits (68), Expect = 0.55
Identities = 13/67 (19%), Positives = 20/67 (29%), Gaps = 21/67 (31%)
Query: 66 VAIAQNVDTGAILMQGFANRDALATTISSRKATFYSR------SR--STLWTKGETSQNF 117
V AQ + Q +ALA + R +R L +F
Sbjct: 413 VQKAQTKE------QADFAIEALAKAK-------FERLFRWILTRVNKALDKTKRQGASF 459
Query: 118 INVQDIF 124
+ + DI
Sbjct: 460 LGILDIA 466
>1qme_A Penicillin-binding protein 2X; peptidoglycan synthesis, resistance,
cell WALL, transmembrane; 2.4A {Streptococcus
pneumoniae} SCOP: d.11.1.1 d.11.1.1 d.175.1.1 e.3.1.1
PDB: 1qmf_A* 1pyy_A* 1rp5_A 1pmd_A 1k25_A 2zc3_B*
2z2l_B* 2z2m_B* 2zc4_B* 2zc3_A* 2z2l_A* 2z2m_A* 2zc4_A*
2zc3_C* 2z2l_C* 2z2m_C* 2zc4_C*
Length = 702
Score = 29.3 bits (66), Expect = 0.92
Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 3/41 (7%)
Query: 46 LQSKVDRLLDSVKWDNKGLAV-AIAQNVDTGAILMQGFANR 85
LQS ++ +D+ + KG + A + TG IL R
Sbjct: 221 LQSFMETQMDAFQEKVKGKYMTATLVSAKTGEIL--ATTQR 259
>2v26_A Myosin VI; calmodulin-binding, nucleotide-binding, membrane,
vanadate, transport, PRE- powerstroke, transition state,
protein transport; HET: ADP; 1.75A {Sus scrofa} PDB:
2bki_A 2bkh_A 3l9i_A 2x51_A 2vb6_A* 2vas_A*
Length = 784
Score = 29.1 bits (66), Expect = 1.1
Identities = 22/92 (23%), Positives = 34/92 (36%), Gaps = 23/92 (25%)
Query: 41 NSNPVLQSKVDRLLDSVKWDNKGLAVAIAQNVDTGAILMQGFANRDALATTISSRKATFY 100
+ + + S R++ + KG + + V+ Q RDALA T+ Y
Sbjct: 378 DQDDLRVSLTTRVMLTTAGGAKGTVIKVPLKVE------QANNARDALAKTV-------Y 424
Query: 101 SR------SR--STLWTKGETSQNFINVQDIF 124
S +R + TS FI V DI
Sbjct: 425 SHLFDHVVNRVNQCFPFE--TSSYFIGVLDIA 454
>2wad_A Penicillin-binding protein 2B; peptidoglycan synthesis, transme
antibiotic resistance, cell shape, peptidoglycan; 2.18A
{Streptococcus pneumoniae} PDB: 2wae_A 2waf_A
Length = 680
Score = 28.7 bits (64), Expect = 1.3
Identities = 16/48 (33%), Positives = 19/48 (39%), Gaps = 13/48 (27%)
Query: 46 LQSKVDRLL----------DSVKWDNKGLAVAIAQNVDTGAIL-MQGF 82
Q VD LL K+ AVA+ N TGA+L M G
Sbjct: 316 FQDSVDALLKSYFNSELGNGGAKYSEGVYAVAL--NPQTGAVLSMSGL 361
>1kk8_A Myosin heavy chain, striated muscle; actin-detached, mechanics of
motor, contractIle PROT; HET: ADP; 2.30A {Argopecten
irradians} SCOP: b.34.3.1 c.37.1.9 PDB: 1kk7_A* 1qvi_A*
1s5g_A* 1sr6_A 1b7t_A* 1kqm_A* 1kwo_A* 1l2o_A* 1dfl_A*
2w4t_C 2w4v_C 2w4w_C 1dfk_A 2ec6_A 2otg_A* 2os8_A*
2ovk_A 2ekv_A 2ekw_A 2oy6_A* ...
Length = 837
Score = 27.7 bits (62), Expect = 3.0
Identities = 18/67 (26%), Positives = 24/67 (35%), Gaps = 22/67 (32%)
Query: 66 VAIAQNVDTGAILMQGFANRDALATTISSRKATFYSR------SR--STLWTKGETSQNF 117
V QN++ Q + ALA ++ Y R R TL TK +
Sbjct: 410 VTKGQNMN------QVVNSVGALAKSL-------YDRMFNWLVRRVNKTLDTK-AKRNYY 455
Query: 118 INVQDIF 124
I V DI
Sbjct: 456 IGVLDIA 462
>3av3_A Phosphoribosylglycinamide formyltransferase; structural genomics,
riken structural genomics/proteomics in RSGI, rossmann
fold; HET: MSE; 1.70A {Geobacillus kaustophilus}
Length = 212
Score = 27.1 bits (61), Expect = 3.1
Identities = 18/72 (25%), Positives = 28/72 (38%), Gaps = 16/72 (22%)
Query: 27 MKRNCLVFASSTESNSNPVLQSKVDR-----------LLDSVKWDNKGLAVAIAQNVDTG 75
MKR VFAS + +N Q+ VD LL + K + A +NV
Sbjct: 3 MKR-LAVFASGSGTN----FQAIVDAAKRGDLPARVALLVCDRPGAKVIERAARENVPAF 57
Query: 76 AILMQGFANRDA 87
+ + ++ A
Sbjct: 58 VFSPKDYPSKAA 69
>1lkx_A Myosin IE heavy chain; myosin motor domain, lever ARM, converter
domain, contractIle protein; HET: ADP; 3.00A
{Dictyostelium discoideum} SCOP: c.37.1.9
Length = 697
Score = 27.1 bits (61), Expect = 4.1
Identities = 13/76 (17%), Positives = 26/76 (34%), Gaps = 22/76 (28%)
Query: 57 VKWDNKGLAVAIAQNVDTGAILMQGFANRDALATTISSRKATFYSR------SR--STLW 108
+ +++ + + Q +RDALA + Y R S+ + +
Sbjct: 327 TGVGKRCSVISVPMDCN------QAAYSRDALAKAL-------YERLFNWLVSKINTIIN 373
Query: 109 TKGETSQNFINVQDIF 124
E I + DI+
Sbjct: 374 CTTE-KGPVIGILDIY 388
>4ds3_A Phosphoribosylglycinamide formyltransferase; structural genomics,
seattle structural genomics center for infectious
disease, ssgcid; 1.85A {Brucella melitensis BV}
Length = 209
Score = 26.7 bits (60), Expect = 4.4
Identities = 14/75 (18%), Positives = 28/75 (37%), Gaps = 23/75 (30%)
Query: 28 KRNCLVFASSTESNSNPVLQSKVDRLLDSVKWDN---------------KGLAVAIAQNV 72
+ ++F S SN +++ L+ + + GLA A A +
Sbjct: 7 RNRVVIFISGGGSN----MEA----LIRAAQAPGFPAEIVAVFSDKAEAGGLAKAEAAGI 58
Query: 73 DTGAILMQGFANRDA 87
T + FA+++A
Sbjct: 59 ATQVFKRKDFASKEA 73
>3ue3_A Septum formation, penicillin binding protein 3, peptidoglycan
synthetase; transpeptidase, transferase; 2.30A
{Acinetobacter}
Length = 554
Score = 26.8 bits (60), Expect = 5.1
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 46 LQSKVDRLLDSVKWDNKGLAV-AIAQNVDTGAIL 78
LQ + R L + N + AIA +V TG IL
Sbjct: 213 LQYIMYRELTAAGVANNARSATAIAVDVKTGEIL 246
>1w7j_A Myosin VA; motor protein, unconventional myosin, myosin V, chicken,
molecular motor, ATPase, ELC, IQ motif, muscle protein,
ATP-binding; HET: ADP; 2A {Gallus gallus} SCOP: b.34.3.1
c.37.1.9 PDB: 1w7i_A* 1oe9_A* 1w8j_A
Length = 795
Score = 26.8 bits (60), Expect = 5.4
Identities = 13/67 (19%), Positives = 19/67 (28%), Gaps = 22/67 (32%)
Query: 66 VAIAQNVDTGAILMQGFANRDALATTISSRKATFYSR------SR--STLWTKGETSQNF 117
+ RDALA I Y+ L + + +F
Sbjct: 387 YIKPISKL------HAINARDALAKHI-------YANLFNWIVDHVNKALHSTVK-QHSF 432
Query: 118 INVQDIF 124
I V DI+
Sbjct: 433 IGVLDIY 439
>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp
contractIle protein-transport protein complex; 24.00A
{Gallus gallus}
Length = 1080
Score = 27.0 bits (60), Expect = 5.6
Identities = 13/67 (19%), Positives = 19/67 (28%), Gaps = 22/67 (32%)
Query: 66 VAIAQNVDTGAILMQGFANRDALATTISSRKATFYSR------SR--STLWTKGETSQNF 117
+ RDALA I Y+ L + + +F
Sbjct: 387 YIKPISKL------HAINARDALAKHI-------YANLFNWIVDHVNKALHSTVK-QHSF 432
Query: 118 INVQDIF 124
I V DI+
Sbjct: 433 IGVLDIY 439
>2ywr_A Phosphoribosylglycinamide formyltransferase; rossmann fold,
structural genomics, NPPSFA; 1.77A {Aquifex aeolicus}
Length = 216
Score = 26.3 bits (59), Expect = 6.4
Identities = 12/76 (15%), Positives = 24/76 (31%), Gaps = 24/76 (31%)
Query: 27 MKRNCLVFASSTESNSNPVLQSKVDRLLDSVKWDN---------------KGLAVAIAQN 71
M + V S SN LQ+ ++D+++ + N
Sbjct: 1 MLK-IGVLVSGRGSN----LQA----IIDAIESGKVNASIELVISDNPKAYAIERCKKHN 51
Query: 72 VDTGAILMQGFANRDA 87
V+ I + F ++
Sbjct: 52 VECKVIQRKEFPSKKE 67
>2f09_A Hypothetical protein YDHA; strand beta-barrel, structural genomics,
ontario centre for structural proteomics, OCSP, unknown
function; NMR {Escherichia coli K12} SCOP: b.61.8.1
Length = 102
Score = 25.1 bits (54), Expect = 7.9
Identities = 10/68 (14%), Positives = 22/68 (32%), Gaps = 3/68 (4%)
Query: 60 DNKGLAVAIAQNVDTGAILMQGFANRDALATTISSRKATFYSRSRSTLWTKGETSQNFIN 119
D K L V + + + + S Y+ W+KG+ + +
Sbjct: 31 DEKPLTVKLNNPRQEVSFVYDN---QLLHLKQGISASGARYTDGIYVFWSKGDEATVYKR 87
Query: 120 VQDIFLDC 127
+ + +C
Sbjct: 88 DRIVLNNC 95
>1p9l_A Dihydrodipicolinate reductase; oxidoreductase, lysine biosynthesis,
NADH binding specificity, TB structural genomics
consortium; HET: NAD PDC PG4; 2.30A {Mycobacterium
tuberculosis} SCOP: c.2.1.3 d.81.1.3 PDB: 1c3v_A* 1yl5_A
1yl7_A* 1yl6_A*
Length = 245
Score = 26.0 bits (58), Expect = 8.9
Identities = 10/30 (33%), Positives = 14/30 (46%)
Query: 54 LDSVKWDNKGLAVAIAQNVDTGAILMQGFA 83
++S +V IA N GA+L FA
Sbjct: 87 VESWLVAKPNTSVLIAPNFAIGAVLSMHFA 116
>3equ_A PBP-2, penicillin-binding protein 2; class B transpeptidase, cell
DIV cell inner membrane, cell membrane, cell shape; HET:
SEP; 2.40A {Neisseria gonorrhoeae} PDB: 3eqv_A*
Length = 542
Score = 26.0 bits (58), Expect = 9.7
Identities = 7/34 (20%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 46 LQSKVDRLLDSVKWDNKGLAV-AIAQNVDTGAIL 78
+Q+ L+ ++ A + + TG IL
Sbjct: 204 IQTLAYEELNKAVEYHQAKAGTVVVLDARTGEIL 237
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.317 0.130 0.383
Gapped
Lambda K H
0.267 0.0839 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,711,185
Number of extensions: 142591
Number of successful extensions: 278
Number of sequences better than 10.0: 1
Number of HSP's gapped: 272
Number of HSP's successfully gapped: 25
Length of query: 196
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 107
Effective length of database: 4,216,824
Effective search space: 451200168
Effective search space used: 451200168
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (24.8 bits)