RPS-BLAST 2.2.22 [Sep-27-2009]
Database: mmdb70
33,805 sequences; 4,956,049 total letters
Searching..................................................done
Query= gi|254780237|ref|YP_003064650.1| DNA-directed RNA polymerase
subunit alpha [Candidatus Liberibacter asiaticus str. psy62]
(340 letters)
>3iyd_A DNA-directed RNA polymerase subunit alpha; transcription,
initiation, class I, activator, RNA polymerase,
holoenzyme, sigma70, open complex, CAP, CRP,
CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli
k-12} (A:49-180)
Length = 132
Score = 156 bits (397), Expect = 3e-39
Identities = 60/132 (45%), Positives = 87/132 (65%), Gaps = 4/132 (3%)
Query: 53 SSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG 112
SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G +T+ K G G
Sbjct: 1 SSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIG 60
Query: 113 VVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA---KHHRTENDPI 168
VTA DI D+E++ P HVIC+L D +A + M + V +G GYVPA H + PI
Sbjct: 61 PVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPI 120
Query: 169 GLITIDALYSPI 180
G + +DA YSP+
Sbjct: 121 GRLLVDACYSPV 132
>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase
holoenzyme, streptolydigin, antibiotic, transcription
regulation; HET: STD; 2.40A {Thermus thermophilus}
(A:48-172)
Length = 125
Score = 149 bits (378), Expect = 5e-37
Identities = 52/126 (41%), Positives = 77/126 (61%), Gaps = 3/126 (2%)
Query: 55 LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI--FKRGPG 112
+ G A+T+V I+ VLHE S+I GV ED+ +IILN+K + ++ S + VT+ GP
Sbjct: 1 IPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELVVRFLNPSLQTVTLLLKAEGPK 60
Query: 113 VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT 172
V A D V D+E++NPD I L+ + ME+ V +G GYVPA+ H + D I I
Sbjct: 61 EVKARDFLPVADVEIMNPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIK-DRINAIP 119
Query: 173 IDALYS 178
+DA++S
Sbjct: 120 VDAVFS 125
>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase,
assemble; 2.50A {Escherichia coli} (A:51-178)
Length = 128
Score = 148 bits (376), Expect = 7e-37
Identities = 57/128 (44%), Positives = 83/128 (64%), Gaps = 4/128 (3%)
Query: 55 LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G +T+ K G G V
Sbjct: 1 MPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPV 60
Query: 115 TAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGL 170
TA DI D+E++ P HVIC+L D +A + M + V +G GYVPA H + PIG
Sbjct: 61 TAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGR 120
Query: 171 ITIDALYS 178
+ +DA YS
Sbjct: 121 LLVDACYS 128
>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase
holoenzyme, streptolydigin, antibiotic, transcription
regulation; HET: STD; 2.40A {Thermus thermophilus}
(A:1-47,A:173-315)
Length = 190
Score = 140 bits (353), Expect = 3e-34
Identities = 47/144 (32%), Positives = 70/144 (48%), Gaps = 2/144 (1%)
Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
L SP+++V++ VE R GQ D DKL++ I TDGS+T +++ A IL++ L F N +
Sbjct: 45 LSSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFSNPQ 104
Query: 236 EPKKEVKEDINVKS--LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
E+ L +EEL LS R + L+ E I + L+ D+
Sbjct: 105 AAAVAAPEEAKEPEAPPEQEEELDLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLK 164
Query: 294 RMANFGRKSLVEIKGVLGTMGLFL 317
+ G +SL EIK L G L
Sbjct: 165 NIPGIGERSLEEIKEALEKKGFTL 188
Score = 50.7 bits (121), Expect = 3e-07
Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 3/48 (6%)
Query: 7 QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSS 54
+K + + EPL RGF TLGN LRR+L+SS
Sbjct: 3 DSKLKAPVFTVR---TQGREYGEFVLEPLERGFGVTLGNPLRRILLSS 47
>1coo_A RNA polymerase alpha subunit; transcription regulation,
nucleotidyl transferase; NMR {Escherichia coli K12} (A:)
Length = 98
Score = 107 bits (269), Expect = 2e-24
Identities = 46/100 (46%), Positives = 69/100 (69%), Gaps = 3/100 (3%)
Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
++ + ++ ++ + F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE +
Sbjct: 1 MDLRDVREPEVKE---EKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVE 57
Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
+L+ N G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 58 LLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 97
>1lb2_B DNA-directed RNA polymerase alpha chain; protein-DNA
complex, gene-regulatory, gene regulation/DNA complex;
HET: CMP; 3.10A {Escherichia coli} (B:)
Length = 84
Score = 105 bits (264), Expect = 7e-24
Identities = 46/80 (57%), Positives = 61/80 (76%)
Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+ N G+KSL EIK VL
Sbjct: 4 FDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLA 63
Query: 312 TMGLFLGMNLPDWPPESIEE 331
+ GL LGM L +WPP SI +
Sbjct: 64 SRGLSLGMRLENWPPASIAD 83
>3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein
complex, cytoplasm, redox-active center, stress
response, transcription; 2.30A {Bacillus subtilis} (B:)
Length = 79
Score = 87.8 bits (218), Expect = 2e-18
Identities = 30/74 (40%), Positives = 43/74 (58%)
Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
+ L +EEL+LSVRS NCL+ I + +L +TE DM+++ N GRKSL E+
Sbjct: 5 KEEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEV 64
Query: 307 KGVLGTMGLFLGMN 320
K L +GL L +
Sbjct: 65 KAKLEELGLGLRKD 78
>1z3e_B DNA-directed RNA polymerase alpha chain; bacterial
transcription regulation, disulfide stress; 1.50A
{Bacillus subtilis} (B:)
Length = 73
Score = 86.6 bits (215), Expect = 5e-18
Identities = 30/71 (42%), Positives = 43/71 (60%)
Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
+ L +EEL+LSVRS NCL+ I + +L +TE DM+++ N GRKSL E+K
Sbjct: 1 MEKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAK 60
Query: 310 LGTMGLFLGMN 320
L +GL L +
Sbjct: 61 LEELGLGLRKD 71
>3iyd_A DNA-directed RNA polymerase subunit alpha; transcription,
initiation, class I, activator, RNA polymerase,
holoenzyme, sigma70, open complex, CAP, CRP,
CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli
k-12} (A:1-48,A:181-246)
Length = 114
Score = 84.4 bits (209), Expect = 2e-17
Identities = 20/65 (30%), Positives = 43/65 (66%)
Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
+++++Y VE+AR Q D DKL + ++T+G+I E+++ A+ IL +QL F++ + ++
Sbjct: 48 LERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQ 107
Query: 240 EVKED 244
++
Sbjct: 108 PEVKE 112
Score = 64.7 bits (158), Expect = 2e-11
Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 3/51 (5%)
Query: 2 IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLM 52
+Q + E +KP ++ Q + EPL RGF HTLGNALRR+L+
Sbjct: 1 MQGSVTEFLKPRLVDIE---QVSSTHAKVTLEPLERGFGHTLGNALRRILL 48
>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase,
assemble; 2.50A {Escherichia coli} (A:1-50,A:179-235)
Length = 107
Score = 82.8 bits (205), Expect = 6e-17
Identities = 23/59 (38%), Positives = 41/59 (69%)
Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
L SP+++++Y VE+AR Q D DKL + ++T+G+I E+++ A+ IL +QL F++
Sbjct: 48 LSSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDL 106
Score = 61.3 bits (149), Expect = 2e-10
Identities = 22/53 (41%), Positives = 31/53 (58%), Gaps = 3/53 (5%)
Query: 2 IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSS 54
+Q + E +KP ++ + Q + EPL RGF HTLGNALR +L+SS
Sbjct: 1 MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRAILLSS 50
>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase,
translation termination, ATP-binding, cytoplasm,
hydrolase, membrane; 2.80A {Schizosaccharomyces pombe}
(A:1-326)
Length = 326
Score = 27.8 bits (61), Expect = 1.9
Identities = 13/69 (18%), Positives = 25/69 (36%), Gaps = 19/69 (27%)
Query: 283 DLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL-----FLGMNLPD----------WPPE 327
DL++R + L + L E +L GL + LP +
Sbjct: 248 DLMKRRQ---LDARDIKVFVLDEADNMLDQQGLGDQSMRIKHLLPRNTQIVLFSATFSER 304
Query: 328 SIEELAKKY 336
+E+ A+++
Sbjct: 305 -VEKYAERF 312
>2j9l_A Chloride channel protein 5; domain, membrane, transport, CBS
domain, CLC, disease mutation, ION channel, ION
transport, transmembrane; HET: ATP; 2.30A {Homo sapiens}
(A:1-114)
Length = 114
Score = 27.9 bits (62), Expect = 2.0
Identities = 8/129 (6%), Positives = 22/129 (17%), Gaps = 21/129 (16%)
Query: 99 DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
++ + V+ + + D + + P
Sbjct: 2 EAKEEFAHKTLAMDVMKPRRNDP-LLTVLTQDSMTV----EDVETIIS---ETTYSGFPV 53
Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
R +G + L + D + + T
Sbjct: 54 VVSRESQRLVGFVLRRDLII---------SIENARKKQDG----VVSTSIIYFTEHSPPL 100
Query: 219 LASRILQDQ 227
+
Sbjct: 101 PPYTPPTLK 109
>1zau_A DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium
tuberculosis} (A:126-246)
Length = 121
Score = 27.9 bits (62), Expect = 2.1
Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 6/47 (12%)
Query: 57 GAAITAVQIDGVLHEISS----IKGVHEDLTDIILNIKGINLKMSGD 99
G A++ V +G L S+ G ED+T I + +++
Sbjct: 1 GVALSLVYREGRLTRASTRGDGRTG--EDVTLNARTIADVPERLTPG 45
>2owo_A DNA ligase; protein/DNA complex, ligase/DNA complex; HET:
DNA OMC AMP; 2.30A {Escherichia coli K12}
(A:1-60,A:117-236)
Length = 180
Score = 27.5 bits (61), Expect = 2.7
Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 3/70 (4%)
Query: 57 GAAITAVQIDGVLHE-ISSIKGVH-EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
G A++ + +GVL + G ED+T + I+ I LK+ G++ RG +
Sbjct: 62 GLAVSILYENGVLVSAATRGDGTTGEDITSNVRTIRAIPLKLHGENIPARLEV-RGEVFL 120
Query: 115 TAGDIQTVND 124
+ +N+
Sbjct: 121 PQAGFEKINE 130
>3jsl_A DNA ligase; NAD+-dependent, DNA damage, DNA repair, DNA
replication, magnesium, manganese, metal-binding, NAD,
zinc; HET: DNA; 1.80A {Staphylococcus aureus} PDB:
3jsn_A* (A:115-227)
Length = 113
Score = 27.1 bits (60), Expect = 3.5
Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 4/48 (8%)
Query: 57 GAAITAVQIDGVLHEISSIKG---VHEDLTDIILNIKGINLKMSGDSH 101
G A++ +DG + + +G ED+T+ + I I LKM +
Sbjct: 1 GLAVSLKYVDGYFVQGLT-RGDGTTGEDITENLKTIHAIPLKMKEPLN 47
>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe} (C:1-38,C:171-297)
Length = 165
Score = 26.7 bits (59), Expect = 4.1
Identities = 11/55 (20%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
+ + M +++ GSI + + RILQ++L + + + +E ++ L
Sbjct: 93 EPRRFYMDVESVGSIPPNEIMVQGLRILQEKLAVLV--RDLDEEQPTQLSANELN 145
>3bac_A DNA ligase; adenylation domain, DNA damage, DNA repair, DNA
replication, NAD; HET: DNA 3B9; 3.00A {Haemophilus
influenzae} (A:56-173)
Length = 118
Score = 26.7 bits (59), Expect = 4.2
Identities = 15/72 (20%), Positives = 32/72 (44%), Gaps = 7/72 (9%)
Query: 57 GAAITAVQIDGVLHEISS----IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG 112
G A++ + ++G L + ++ G ED+T I I+ + L++ D+ RG
Sbjct: 1 GLAVSILYVNGELTQAATRGDGTTG--EDITANIRTIRNVPLQLLTDNPPARLEV-RGEV 57
Query: 113 VVTAGDIQTVND 124
+ + +N
Sbjct: 58 FMPHAGFERLNK 69
>1ta8_A DNA ligase, NAD-dependent; nucleotidyl transferase fold;
HET: DNA NMN; 1.80A {Enterococcus faecalis V583}
(A:64-76,A:122-254)
Length = 146
Score = 25.6 bits (56), Expect = 8.8
Identities = 9/43 (20%), Positives = 24/43 (55%), Gaps = 4/43 (9%)
Query: 57 GAAITAVQIDGVLHEISSIKG---VHEDLTDIILNIKGINLKM 96
G AI+ +GV ++ +G V E++T+ + ++ + +++
Sbjct: 15 GLAISLRYENGVFVRGAT-RGDGTVGENITENLRTVRSVPMRL 56
>1g8f_A Sulfate adenylyltransferase; alpha-beta protein,
beta-barrel, rossmann-fold, kinase fold; 1.95A
{Saccharomyces cerevisiae} (A:169-391)
Length = 223
Score = 25.7 bits (56), Expect = 8.9
Identities = 7/27 (25%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 315 LFLGMNLPDW--PPESIEELAKKYEDK 339
L +G +P+W PE ++ L + +
Sbjct: 197 LRVGGEIPEWFSYPEVVKILRESNPPR 223
>1b04_A Protein (DNA ligase); DNA replication; 2.80A {Bacillus
stearothermophilus} (A:117-248)
Length = 132
Score = 25.6 bits (56), Expect = 9.1
Identities = 10/46 (21%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 57 GAAITAVQIDGVLHEISSIKG---VHEDLTDIILNIKGINLKMSGD 99
G A++ DG + ++ +G ED+T+ + I+ + L++
Sbjct: 1 GLAVSVRYEDGYFVQGAT-RGDGTTGEDITENLKTIRSLPLRLKEP 45
>1r6x_A ATP:sulfate adenylyltransferase; APS kinase-like domain;
1.40A {Saccharomyces cerevisiae} (A:168-395)
Length = 228
Score = 25.8 bits (56), Expect = 9.3
Identities = 7/27 (25%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 315 LFLGMNLPDW--PPESIEELAKKYEDK 339
L +G +P+W PE ++ L + +
Sbjct: 197 LRVGGEIPEWFSYPEVVKILRESNPPR 223
Database: mmdb70
Posted date: Jun 20, 2010 3:12 AM
Number of letters in database: 4,956,049
Number of sequences in database: 33,805
Lambda K H
0.317 0.136 0.386
Gapped
Lambda K H
0.267 0.0623 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 2,535,118
Number of extensions: 114402
Number of successful extensions: 325
Number of sequences better than 10.0: 1
Number of HSP's gapped: 316
Number of HSP's successfully gapped: 37
Length of query: 340
Length of database: 4,956,049
Length adjustment: 89
Effective length of query: 251
Effective length of database: 1,947,404
Effective search space: 488798404
Effective search space used: 488798404
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.2 bits)