RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780440|ref|YP_003064853.1| transcription elongation
factor GreA [Candidatus Liberibacter asiaticus str. psy62]
(158 letters)
>1grj_A GREA protein; transcript elongation factor, transcript cleavage
factor, transcription regulation; 2.20A {Escherichia
coli} SCOP: a.2.1.1 d.26.1.2
Length = 158
Score = 145 bits (366), Expect = 6e-36
Identities = 71/157 (45%), Positives = 113/157 (71%), Gaps = 1/157 (0%)
Query: 3 DKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGR 62
IP+T +G +K+++EL + + RP II AI+EAR +GDL ENAEY AA+E Q EGR
Sbjct: 2 QAIPMTLRGAEKLREELDFLKSVRRPEIIAAIAEAREHGDLKENAEYHAAREQQGFCEGR 61
Query: 63 MAELENIITRAEVIDISTMSGD-RIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVS 121
+ ++E ++ A+VID++ M + R+ FGATV+++ +S +++ Y+IVGD EAD + L+S
Sbjct: 62 IKDIEAKLSNAQVIDVTKMPNNGRVIFGATVTVLNLDSDEEQTYRIVGDDEADFKQNLIS 121
Query: 122 ISSPIARALIGKELGDIISVNAPGGEKTYEILQVLWI 158
++SPIAR LIGKE D++ + PGGE +E+++V ++
Sbjct: 122 VNSPIARGLIGKEEDDVVVIKTPGGEVEFEVIKVEYL 158
>2f23_A Anti-cleavage anti-GREA transcription factor GFH1; anti-GREA GFH1
thermus thermophilus; 1.60A {Thermus thermophilus HB27}
SCOP: a.2.1.1 d.26.1.2 PDB: 2eul_A 2etn_A
Length = 156
Score = 127 bits (321), Expect = 9e-31
Identities = 43/157 (27%), Positives = 90/157 (57%), Gaps = 5/157 (3%)
Query: 1 MVDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNE 60
M ++ +T G++++ Q+L R++E K + E D +++ +AAK+ + E
Sbjct: 1 MAREVKLTKAGYERLMQQLE-RERERLQEATKILQELMESSDDYDDSGLEAAKQEKARIE 59
Query: 61 GRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADV--QSG 118
R+ LE+I++R + + SG+ I G+ V L + SG++ + Q+V EA+V
Sbjct: 60 ARIDSLEDILSR--AVILEEGSGEVIGLGSVVELEDPLSGERLSVQVVSPAEANVLDTPM 117
Query: 119 LVSISSPIARALIGKELGDIISVNAPGGEKTYEILQV 155
+S +SP+ +AL+G +GD++S++ P G++ + ++ +
Sbjct: 118 KISDASPMGKALLGHRVGDVLSLDTPKGKREFRVVAI 154
>2p4v_A Transcription elongation factor GREB; transcript cleavage,
GRE-factors, RNA polymerase; 2.60A {Escherichia coli}
Length = 158
Score = 124 bits (312), Expect = 8e-30
Identities = 53/155 (34%), Positives = 90/155 (58%), Gaps = 1/155 (0%)
Query: 4 KIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRM 63
VT +G++K++QEL + +EERP + K ++ A + GD SENA+YQ K+ + R+
Sbjct: 3 TPLVTREGYEKLKQELNYLWREERPEVTKKVTWAASLGDRSENADYQYNKKRLREIDRRV 62
Query: 64 AELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSIS 123
L + +++D S ++ FGA V +E + G ++IVG E + +SI
Sbjct: 63 RYLTKCMENLKIVDYSPQQEGKVFFGAWV-EIENDDGVTHRFRIVGYDEIFGRKDYISID 121
Query: 124 SPIARALIGKELGDIISVNAPGGEKTYEILQVLWI 158
SP+ARAL+ KE+GD+ VN P GE ++ + + ++
Sbjct: 122 SPMARALLKKEVGDLAVVNTPAGEASWYVNAIEYV 156
>2pn0_A Prokaryotic transcription elongation factor GREA/GREB; structural
genomics, APC6349, PSI-2, protein structure initiative;
HET: MSE; 1.70A {Nitrosomonas europaea}
Length = 141
Score = 113 bits (284), Expect = 2e-26
Identities = 32/134 (23%), Positives = 57/134 (42%), Gaps = 9/134 (6%)
Query: 25 EERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGD 84
+P+I+ + +A L E A +LE + RAEV+D +
Sbjct: 4 SIKPKIMISSLDAERLEILLETLSQNAFPGRD--------DLEAELARAEVVDPEEIPPT 55
Query: 85 RIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAP 144
+ +TV ++S ++ +V ++ D +SI +P+ AL+G GD I P
Sbjct: 56 VVTMNSTVRFRVESSAEEFCLTLVYPKDVDTSGEKISILAPVGSALLGLAQGDEIEWPKP 115
Query: 145 -GGEKTYEILQVLW 157
GG I++V +
Sbjct: 116 GGGVLRVRIVEVTY 129
>3bmb_A Regulator of nucleoside diphosphate kinase; RNA polymerase,
elongation factor, anti-GRE factor, RNA binding protein;
1.91A {Escherichia coli}
Length = 136
Score = 111 bits (280), Expect = 5e-26
Identities = 29/133 (21%), Positives = 51/133 (38%), Gaps = 9/133 (6%)
Query: 26 ERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDR 85
RP II +A L E Y L + RA++ M D
Sbjct: 2 SRPTIIINDLDAERIDILLEQPAYAGLPIAD--------ALNAELDRAQMCSPEEMPHDV 53
Query: 86 IAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPG 145
+ + V + G+ + +V + + +S+ +P+ AL+G +GD I PG
Sbjct: 54 VTMNSRVKFRNLSDGEVRVRTLVYPAKMTDSNTQLSVMAPVGAALLGLRVGDSIHWELPG 113
Query: 146 G-EKTYEILQVLW 157
G E+L++ +
Sbjct: 114 GVATHLEVLELEY 126
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 37.2 bits (86), Expect = 0.002
Identities = 27/137 (19%), Positives = 44/137 (32%), Gaps = 38/137 (27%)
Query: 24 QEERPRIIKAISEARAYGD-----LSENAEYQAAKE----L------QNLNEGRMAELEN 68
+ +IK AR S +A ++A E L Q + EL
Sbjct: 116 LVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEEL-- 173
Query: 69 IITRAEVIDI-STMSGDRIAFGATV--SLVEKNSGDKKNYQIVGDQEADVQSGLVS---- 121
++ + GD I F A L+ +K + Q ++ L +
Sbjct: 174 ----RDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFT----QGLNILEWLENPSNT 225
Query: 122 ------ISSPIARALIG 132
+S PI+ LIG
Sbjct: 226 PDKDYLLSIPISCPLIG 242
Score = 26.4 bits (58), Expect = 3.3
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 10/52 (19%)
Query: 45 ENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDRIAFGATVSLVE 96
EN +Y AA +L+ L+ + + N I + + IDI I ++SL E
Sbjct: 1849 ENQQYVAAGDLRALDT--VTNVLNFI-KLQKIDI-------IELQKSLSLEE 1890
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 33.0 bits (74), Expect = 0.034
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 14/66 (21%)
Query: 13 DKIQQE----LRWRQQEERPRI--IKAISEA-------RAYGDLSENAEYQAAKELQNLN 59
D++ QE +WR+ E+R R+ + A S+ +A DL E + Q+ + +N
Sbjct: 78 DRLTQEPESIRKWRE-EQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKI 136
Query: 60 EGRMAE 65
R+A+
Sbjct: 137 NNRIAD 142
Score = 27.6 bits (60), Expect = 1.4
Identities = 25/114 (21%), Positives = 44/114 (38%), Gaps = 39/114 (34%)
Query: 3 DKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGR 62
D++ + K ++E R R QE + A S+ + + +A K+L+ N+ +
Sbjct: 78 DRLTQEPESIRKWREEQRKRLQE-----LDAASKV-----MEQEWREKAKKDLEEWNQRQ 127
Query: 63 MAELE-NIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADV 115
++E N I +RIA DK YQ +AD+
Sbjct: 128 SEQVEKNKIN------------NRIA-------------DKAFYQ---QPDADI 153
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 31.9 bits (71), Expect = 0.066
Identities = 8/28 (28%), Positives = 13/28 (46%), Gaps = 1/28 (3%)
Query: 10 KGFDKIQQELRWRQQEERPRI-IKAISE 36
+ K+Q L+ + P + IKA E
Sbjct: 20 QALKKLQASLKLYADDSAPALAIKATME 47
Score = 31.9 bits (71), Expect = 0.072
Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 16/45 (35%)
Query: 48 EYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDRIAFGATV 92
E QA K+LQ A L+ A+ D S +A AT+
Sbjct: 18 EKQALKKLQ-------ASLK---LYAD--D----SAPALAIKATM 46
>3n6r_A Propionyl-COA carboxylase, alpha subunit; protein complex,
biotin-dependent carboxylase, ligase; HET: BTI; 3.20A
{Ruegeria pomeroyi}
Length = 681
Score = 31.1 bits (70), Expect = 0.11
Identities = 15/67 (22%), Positives = 27/67 (40%), Gaps = 17/67 (25%)
Query: 28 PRIIKAISEARA------YGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTM 81
+++ AI A YG LSEN+++ A+ L+ + + I+
Sbjct: 64 DKVMAAIRATGAQAVHPGYGFLSENSKF--AEALEA------EGVIFVGPPKGAIE---A 112
Query: 82 SGDRIAF 88
GD+I
Sbjct: 113 MGDKITS 119
>3hbl_A Pyruvate carboxylase; TIM barrel, ligase; HET: BTI ADP; 2.71A
{Staphylococcus aureus subsp} PDB: 3bg5_A* 3ho8_A*
3hb9_A*
Length = 1150
Score = 28.8 bits (64), Expect = 0.57
Identities = 17/67 (25%), Positives = 26/67 (38%), Gaps = 17/67 (25%)
Query: 28 PRIIKAISEARA------YGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTM 81
RII +A YG LSEN ++ A+ ++ I E +D M
Sbjct: 67 ERIIDVAKQANVDAIHPGYGFLSENEQF--ARRCAE------EGIKFIGPHLEHLD---M 115
Query: 82 SGDRIAF 88
GD++
Sbjct: 116 FGDKVKA 122
>3jrx_A Acetyl-COA carboxylase 2; BC domain, soraphen A, alternative
splicing, ATP-binding, biotin, fatty acid biosynthesis,
ligase, lipid synthesis; HET: S1A; 2.50A {Homo sapiens}
PDB: 3jrw_A*
Length = 587
Score = 28.1 bits (62), Expect = 0.91
Identities = 11/67 (16%), Positives = 20/67 (29%), Gaps = 17/67 (25%)
Query: 28 PRIIKAISEARA------YGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTM 81
I+ +G SEN + + L + + +E +
Sbjct: 129 ELIVDIAKRIPVQAVWAGWGHASENPKL--PELLCK------NGVAFLGPPSEAMW---A 177
Query: 82 SGDRIAF 88
GD+IA
Sbjct: 178 LGDKIAS 184
>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix
hairpin helix, NER, hydrolase; 1.50A {Thermotoga
maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A
Length = 220
Score = 28.1 bits (62), Expect = 0.98
Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 5/39 (12%)
Query: 46 NAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGD 84
+A +EL L +++ R E IDIS + G
Sbjct: 3 GLRKEALEELMKL-----LNMKDFPYRIEGIDISHLQGK 36
>1wle_A Seryl-tRNA synthetase; ligase; HET: SRP; 1.65A {Bos taurus}
Length = 501
Score = 28.2 bits (62), Expect = 0.99
Identities = 14/73 (19%), Positives = 33/73 (45%), Gaps = 5/73 (6%)
Query: 2 VDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEG 61
+ I T + ++++++R +EE+ + +A+ D N++ Q + Q+L
Sbjct: 69 LPGIISTWQELRQLREQIR-SLEEEKEAVTEAVRALVVNQD---NSQVQQDPQYQSLRA- 123
Query: 62 RMAELENIITRAE 74
R E+ +T
Sbjct: 124 RGREIRKQLTLLY 136
>2qf7_A Pyruvate carboxylase protein; multi-domain, multi-functional,
biotin-dependent, ligase; HET: KCX COA SAP; 2.00A
{Rhizobium etli cfn 42}
Length = 1165
Score = 27.8 bits (61), Expect = 1.2
Identities = 13/67 (19%), Positives = 25/67 (37%), Gaps = 17/67 (25%)
Query: 28 PRIIKAISEARA------YGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTM 81
+I+ + A YG LSE+ E+ A + I +A+ +
Sbjct: 83 DEVIRVAKLSGADAIHPGYGLLSESPEFVDACNKAGIIF--------IGPKADTMR---Q 131
Query: 82 SGDRIAF 88
G+++A
Sbjct: 132 LGNKVAA 138
>1w96_A ACC, acetyl-coenzyme A carboxylase; ligase, obesity, diabetes,
fatty acid metabolism, structure-based drug design; HET:
S1A; 1.8A {Saccharomyces cerevisiae} SCOP: b.84.2.1
c.30.1.1 d.142.1.2 PDB: 1w93_A
Length = 554
Score = 26.7 bits (58), Expect = 2.6
Identities = 6/38 (15%), Positives = 8/38 (21%), Gaps = 6/38 (15%)
Query: 28 PRIIKAISEARA------YGDLSENAEYQAAKELQNLN 59
I+ A +G SEN
Sbjct: 120 DLIVDIAERADVDAVWAGWGHASENPLLPEKLSQSKRK 157
>3krb_A Aldose reductase; ssgcid, SBRI, emerald biostructures, university
of washington, NIH, niaid, oxidoreductase, structural
genomics; HET: NAP; 1.75A {Giardia lamblia atcc 50803}
Length = 334
Score = 25.7 bits (55), Expect = 4.6
Identities = 12/60 (20%), Positives = 23/60 (38%), Gaps = 4/60 (6%)
Query: 10 KGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENI 69
KG L W ++ + I +++ + N E+Q L++ M + NI
Sbjct: 258 KGTSPHCVALAWHVKKWNTSMYSVIPKSQTPARIEANF---KCTEVQ-LSDDDMDAINNI 313
>3ir3_A HTD2, 3-hydroxyacyl-thioester dehydratase 2; structural genomics,
structural genomics consortium, SGC, lyase; 1.99A {Homo
sapiens}
Length = 148
Score = 25.9 bits (56), Expect = 4.9
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 56 QNLNEGRMAELENIITRAEVIDISTMSGDR 85
++ G AEL T+ +V S ++GD
Sbjct: 14 MHIKVGDRAELRRAFTQTDVATFSELTGDV 43
>1omo_A Alanine dehydrogenase; two-domain, beta-sandwich-dimer,
rossmann-fold NAD domain, human MU crystallin homolog;
HET: NAD; 2.32A {Archaeoglobus fulgidus} SCOP: c.2.1.13
PDB: 1vll_A
Length = 322
Score = 25.2 bits (54), Expect = 7.9
Identities = 21/129 (16%), Positives = 45/129 (34%), Gaps = 18/129 (13%)
Query: 42 DLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMS------GDRIAFGATVSLV 95
D+ E A + ++ + +R +V+ +T S + + G ++ +
Sbjct: 157 DVREKAAKKFVSYCEDRGISASVQPAEEASRCDVLVTTTPSRKPVVKAEWVEEGTHINAI 216
Query: 96 EKNSGD---------KKNYQIVGDQEADVQSGLVSI---SSPIARALIGKELGDIISVNA 143
+ KK +V D E G +++ I + +G++I+
Sbjct: 217 GADGPGKQELDVEILKKAKIVVDDLEQAKHGGEINVAVSKGVIGVEDVHATIGEVIAGLK 276
Query: 144 PGGEKTYEI 152
G E EI
Sbjct: 277 DGRESDEEI 285
>3glk_A Acetyl-COA carboxylase 2; ATP binding, alternative splicing,
ATP-binding, biotin, fatty acid biosynthesis, ligase,
lipid synthesis, manganese; 2.10A {Homo sapiens} PDB:
3gid_A 2hjw_A
Length = 540
Score = 24.8 bits (53), Expect = 8.5
Identities = 5/27 (18%), Positives = 8/27 (29%), Gaps = 6/27 (22%)
Query: 28 PRIIKAISEARA------YGDLSENAE 48
I+ +G SEN +
Sbjct: 113 ELIVDIAKRIPVQAVWAGWGHASENPK 139
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.312 0.131 0.354
Gapped
Lambda K H
0.267 0.0584 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,292,198
Number of extensions: 55012
Number of successful extensions: 173
Number of sequences better than 10.0: 1
Number of HSP's gapped: 165
Number of HSP's successfully gapped: 32
Length of query: 158
Length of database: 5,693,230
Length adjustment: 85
Effective length of query: 73
Effective length of database: 3,632,490
Effective search space: 265171770
Effective search space used: 265171770
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.5 bits)