RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780440|ref|YP_003064853.1| transcription elongation
factor GreA [Candidatus Liberibacter asiaticus str. psy62]
(158 letters)
>gnl|CDD|178936 PRK00226, greA, transcription elongation factor GreA; Reviewed.
Length = 157
Score = 212 bits (542), Expect = 4e-56
Identities = 85/155 (54%), Positives = 117/155 (75%)
Query: 1 MVDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNE 60
M+ KIP+T +G++K+++EL + ERP II+AI+EAR +GDLSENAEY AAKE Q E
Sbjct: 1 MMKKIPMTQEGYEKLEEELEELKTVERPEIIEAIAEAREHGDLSENAEYHAAKEEQGFIE 60
Query: 61 GRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLV 120
GR+ ELE+ ++ AEVID S +SG ++ FG+TV+L + ++ +++ YQIVG EAD + G +
Sbjct: 61 GRIRELEDKLSNAEVIDPSKLSGGKVKFGSTVTLKDLDTDEEETYQIVGSDEADPKQGKI 120
Query: 121 SISSPIARALIGKELGDIISVNAPGGEKTYEILQV 155
SI SPIARALIGK++GD + V PGGE YEIL V
Sbjct: 121 SIESPIARALIGKKVGDTVEVTTPGGEYEYEILSV 155
>gnl|CDD|130529 TIGR01462, greA, transcription elongation factor GreA. In the
Chlamydias and some spirochetes, the region described by
this model is found as the C-terminal region of a much
larger protein.
Length = 151
Score = 180 bits (458), Expect = 2e-46
Identities = 75/150 (50%), Positives = 114/150 (76%)
Query: 6 PVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAE 65
P+T +G++K+++EL + + +RP I + I+EAR +GDLSENAEY AAKE Q NEGR+AE
Sbjct: 1 PLTQEGYEKLKEELEYLKTVKRPEISEEIAEAREHGDLSENAEYHAAKEEQGFNEGRIAE 60
Query: 66 LENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSP 125
LE+++ A+VID S +S D + FG+TV++ + ++G+++ Y IVG EAD + G +SI SP
Sbjct: 61 LEDLLANAQVIDDSKLSTDVVGFGSTVTIKDLDTGEEETYTIVGSWEADPKEGKISIDSP 120
Query: 126 IARALIGKELGDIISVNAPGGEKTYEILQV 155
+ +ALIGK++GD++ V P GEK YEIL++
Sbjct: 121 LGKALIGKKVGDVVEVQTPKGEKEYEILKI 150
>gnl|CDD|179345 PRK01885, greB, transcription elongation factor GreB; Reviewed.
Length = 157
Score = 124 bits (313), Expect = 1e-29
Identities = 56/151 (37%), Positives = 92/151 (60%), Gaps = 5/151 (3%)
Query: 7 VTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNE--GRMA 64
+T +G+ +++QEL + +EERP + + +S A + GD SENA+Y K+ L E R+
Sbjct: 7 ITREGYARLKQELDYLWREERPEVTQKVSWAASLGDRSENADYIYGKKR--LREIDRRVR 64
Query: 65 ELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISS 124
L + +V+D S ++ FGA V + E G++K ++IVG E D + G +SI S
Sbjct: 65 FLTKRLENLKVVDYSPQQEGKVFFGAWVEI-ENEDGEEKRFRIVGPDEIDGRKGYISIDS 123
Query: 125 PIARALIGKELGDIISVNAPGGEKTYEILQV 155
P+ARAL+ KE+GD ++VN P GE + + ++
Sbjct: 124 PMARALLKKEVGDEVTVNTPAGEAEWYVNEI 154
>gnl|CDD|130528 TIGR01461, greB, transcription elongation factor GreB. The GreA
and GreB transcription elongation factors enable to
continuation of RNA transcription past template-encoded
arresting sites. Among the Proteobacteria, distinct
clades of GreA and GreB are found. GreB differs
functionally in that it releases larger
oligonucleotides. This model describes proteobacterial
GreB.
Length = 156
Score = 109 bits (273), Expect = 4e-25
Identities = 54/152 (35%), Positives = 91/152 (59%), Gaps = 1/152 (0%)
Query: 7 VTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAEL 66
+T +G++K++QEL + +EERP + + ++ A + GD SENA+YQ K+ + R+ L
Sbjct: 5 ITPEGYEKLKQELNYLWREERPEVTQKVTWAASLGDRSENADYQYGKKRLREIDRRVRFL 64
Query: 67 ENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPI 126
+ +V+D S ++ FGA V L E + G ++IVG E D + +SI SP+
Sbjct: 65 TKRLENLKVVDYSPQQEGKVFFGAWVEL-ENDDGVTHRFRIVGYDEIDGRKNYISIDSPL 123
Query: 127 ARALIGKELGDIISVNAPGGEKTYEILQVLWI 158
ARAL+ KE+GD + VN P GE ++ + + ++
Sbjct: 124 ARALLKKEVGDEVVVNTPAGEASWYVNAIEYV 155
>gnl|CDD|184804 PRK14720, PRK14720, transcript cleavage factor/unknown domain
fusion protein; Provisional.
Length = 906
Score = 102 bits (255), Expect = 6e-23
Identities = 51/149 (34%), Positives = 89/149 (59%)
Query: 7 VTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAEL 66
VT + +K ++EL + E P K I EA+ GDL ENAEY+AAKE Q + + L
Sbjct: 752 VTRRALNKKKKELEHLKDVEMPENSKDIGEAQELGDLRENAEYKAAKEKQQQLQAALKRL 811
Query: 67 ENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPI 126
E I A+++D++ + ++ FG V L +++G++++Y I+G E+D + G++S SP+
Sbjct: 812 EAEIDSAKILDLTDVKTSKVGFGTKVKLKNEDTGEEESYSILGPWESDPEEGIISYQSPL 871
Query: 127 ARALIGKELGDIISVNAPGGEKTYEILQV 155
++L+GK+ GD + E Y +L++
Sbjct: 872 GKSLLGKKEGDSLEFVINDTETRYTVLKI 900
>gnl|CDD|180531 PRK06330, PRK06330, transcript cleavage factor/unknown domain
fusion protein; Validated.
Length = 718
Score = 75.6 bits (186), Expect = 5e-15
Identities = 49/148 (33%), Positives = 83/148 (56%), Gaps = 5/148 (3%)
Query: 8 TSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELE 67
TS+ F +++ +L+ +E K I +ARA GDL EN+EY+ A E + + + L
Sbjct: 570 TSESFTRMKNKLQSLVGKEMVENAKEIEDARALGDLRENSEYKFALEKRARLQEEIRVLS 629
Query: 68 NIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIA 127
I RA ++ + D++ G V L E + GDK Y I+G +AD + ++S+ S +A
Sbjct: 630 EEINRARILTKDDVFTDKVGVGCKVVL-EDDQGDKVCYTILGPWDADPDNKILSLKSKLA 688
Query: 128 RALIGKELGDIISVNAPGGEKTYEILQV 155
+ ++GK++GD SV G K Y+I ++
Sbjct: 689 QEMLGKKVGD--SVQFQG--KKYKISRI 712
>gnl|CDD|180535 PRK06342, PRK06342, transcription elongation factor regulatory
protein; Validated.
Length = 160
Score = 65.1 bits (159), Expect = 8e-12
Identities = 41/118 (34%), Positives = 69/118 (58%), Gaps = 15/118 (12%)
Query: 47 AEYQAAKELQNLNEGRMAE---------LENIITRAEVIDISTMSGDRIAFGATVSLVEK 97
A Y+AA+ ++++NE R L A+++ S D +AFG+TV+ +
Sbjct: 48 AAYEAAQAIEDVNERRRQMARPLRDLRYLAARRRTAQLMPDPA-STDVVAFGSTVTF-SR 105
Query: 98 NSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQV 155
+ G + Y+IVG+ EAD ++G +S SP+ARAL+GK +GD++SV G + EI+ +
Sbjct: 106 DDGRVQTYRIVGEDEADPKAGSISYVSPVARALMGKAVGDVVSV----GGQELEIIAI 159
>gnl|CDD|180236 PRK05753, PRK05753, nucleoside diphosphate kinase regulator;
Provisional.
Length = 137
Score = 49.9 bits (120), Expect = 3e-07
Identities = 39/134 (29%), Positives = 66/134 (49%), Gaps = 15/134 (11%)
Query: 27 RPRIIKAISE---ARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSG 83
+P II I+E R L E + + LN AEL RA+V+ + M
Sbjct: 4 KPTII--INELDAERLDR-LLEQPAFAGPPIAEALN----AEL----DRAQVVPPAEMPA 52
Query: 84 DRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNA 143
D + + V + +SG+++ +V +AD G +S+ +P+ AL+G +G I
Sbjct: 53 DVVTMNSRVRFRDLSSGEERVRTLVYPADADDSEGQLSVLAPVGAALLGLSVGQSIDWPL 112
Query: 144 PGGEKTY-EILQVL 156
PGG++T+ E+L+V
Sbjct: 113 PGGKETHLEVLEVE 126
>gnl|CDD|180307 PRK05892, PRK05892, nucleoside diphosphate kinase regulator;
Provisional.
Length = 158
Score = 44.0 bits (104), Expect = 2e-05
Identities = 36/147 (24%), Positives = 68/147 (46%), Gaps = 10/147 (6%)
Query: 13 DKIQQELRWRQQEERPRIIKAISEARAYGDLSENAE-YQAAKELQNLNEGRMAELENIIT 71
D ++ EL R + R R+ +++ GD + AE Q A EL L++ R+ EL+ +
Sbjct: 14 DHLEAELA-RLRARRDRLAVEVNDRGMIGDHGDQAEAIQRADELARLDD-RINELDRRLR 71
Query: 72 RAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVG-DQEADV--QSGLVSISSPIAR 128
+ + G V+L G+ + ++ +E V ++ ++ SP+ +
Sbjct: 72 TGP---TPWSGSETLPGGTEVTL-RFPDGEVETMHVISVVEETPVGREAETLTADSPLGQ 127
Query: 129 ALIGKELGDIISVNAPGGEKTYEILQV 155
AL G + GD ++ + P G E+L V
Sbjct: 128 ALAGHQAGDTVTYSTPQGPAQVELLAV 154
>gnl|CDD|179046 PRK00488, pheS, phenylalanyl-tRNA synthetase subunit alpha;
Validated.
Length = 339
Score = 30.1 bits (69), Expect = 0.27
Identities = 20/70 (28%), Positives = 27/70 (38%), Gaps = 19/70 (27%)
Query: 25 EERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELE----NIITRAEVIDIST 80
EER I+E + ++ E R ELE N AE ID+ T
Sbjct: 52 EERKEAGALINELKQ--------------AIEAALEERKEELEAAALNARLAAETIDV-T 96
Query: 81 MSGDRIAFGA 90
+ G RI G+
Sbjct: 97 LPGRRIELGS 106
>gnl|CDD|179065 PRK00558, uvrC, excinuclease ABC subunit C; Validated.
Length = 598
Score = 29.7 bits (68), Expect = 0.31
Identities = 21/72 (29%), Positives = 29/72 (40%), Gaps = 16/72 (22%)
Query: 45 ENAEYQAAKEL--QNLNEGRMAE------LENIITRAEVIDISTMSGDRIAFGATV-SLV 95
+NA ++L Q+ + + E L R E DIS + G ATV S+V
Sbjct: 350 KNAREALERKLSDQSTQQQALEELAELLGLPEPPYRIECFDISHIQGT-----ATVASMV 404
Query: 96 --EKNSGDKKNY 105
E DK Y
Sbjct: 405 VFEDGGPDKSEY 416
>gnl|CDD|165508 PHA03249, PHA03249, DNA packaging tegument protein UL25;
Provisional.
Length = 653
Score = 27.7 bits (61), Expect = 1.2
Identities = 21/94 (22%), Positives = 36/94 (38%), Gaps = 16/94 (17%)
Query: 6 PVTSKGFD----KIQQELRWRQQEERPRIIKAISEARAYGDL-------SENAEYQAAKE 54
VT + ++ +ELR R E P + + R Y L + A Y +
Sbjct: 326 AVTDGQYQACLRRLDEELRKRGTTESPSLTEVYETLRDYNVLFPIAHYTNRGALYLYRQN 385
Query: 55 LQNLNEG-----RMAELENIITRAEVIDISTMSG 83
LQ LN G ++ E + + D++ + G
Sbjct: 386 LQKLNNGHRGVLKLLSSEKLNEEHTLNDLAFLVG 419
>gnl|CDD|169417 PRK08384, PRK08384, thiamine biosynthesis protein ThiI;
Provisional.
Length = 381
Score = 26.5 bits (58), Expect = 3.4
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 121 SISSPIARALIGKELGDIISVNAPGGEKTYEILQVLW 157
I SP+A L+ K ++I V+ GEKT E ++ +W
Sbjct: 190 GIDSPVAAFLMMKRGVEVIPVHIYMGEKTLEKVRKIW 226
>gnl|CDD|182393 PRK10343, PRK10343, RNA-binding protein YhbY; Provisional.
Length = 97
Score = 25.8 bits (56), Expect = 5.3
Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 58 LNEGRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVG 109
L EG +AE+E + E+I + + DR V + + +G N Q++G
Sbjct: 29 LTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETG-ACNVQVIG 79
>gnl|CDD|162465 TIGR01652, ATPase-Plipid, phospholipid-translocating P-type ATPase,
flippase. This model describes the P-type ATPase
responsible for transporting phospholipids from one
leaflet of bilayer membranes to the other. These ATPases
are found only in eukaryotes.
Length = 1057
Score = 25.8 bits (57), Expect = 5.5
Identities = 15/63 (23%), Positives = 23/63 (36%), Gaps = 5/63 (7%)
Query: 95 VEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDI-ISVNAPGGEKTYEIL 153
+ ++ YQ EA LV + + + I + + G K YEIL
Sbjct: 457 FNDDGPEEITYQAASPDEA----ALVKAARDVGFVFFERTPKSISLLIEMHGETKEYEIL 512
Query: 154 QVL 156
VL
Sbjct: 513 NVL 515
>gnl|CDD|149497 pfam08459, UvrC_HhH_N, UvrC Helix-hairpin-helix N-terminal. This
domain is found in the C subunits of the bacterial and
archaeal UvrABC system which catalyses nucleotide
excision repair in a multi-step process. UvrC catalyses
the first incision on the fourth or fifth phosphodiester
bond 3' and on the eighth phosphodiester bond 5' from
the damage that is to be excised. The domain described
here is found to the N-terminus of a helix hairpin helix
(pfam00633) motif and also co-occurs with the pfam01541
catalytic domain which is found at the N-terminus of the
same proteins.
Length = 154
Score = 25.5 bits (57), Expect = 6.3
Identities = 15/44 (34%), Positives = 18/44 (40%), Gaps = 8/44 (18%)
Query: 65 ELENIITRAEVIDISTMSGDRIAFGATV-SLV--EKNSGDKKNY 105
L + R E DIS + G TV S+V E DK Y
Sbjct: 6 GLPKLPHRIECFDISHIQGT-----DTVGSMVVFEDGKPDKSEY 44
>gnl|CDD|185296 PRK15398, PRK15398, aldehyde dehydrogenase EutE; Provisional.
Length = 465
Score = 25.6 bits (57), Expect = 6.5
Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 5/47 (10%)
Query: 16 QQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGR 62
QQ + + R RII AI EA L +AE A ++ GR
Sbjct: 49 QQRYQQKSLAMRQRIIDAIREA-----LLPHAEELAELAVEETGMGR 90
>gnl|CDD|162462 TIGR01647, ATPase-IIIA_H, plasma-membrane proton-efflux P-type
ATPase. This model describes the plasma membrane proton
efflux P-type ATPase found in plants, fungi, protozoa,
slime molds and archaea. The best studied representative
is from yeast.
Length = 755
Score = 25.4 bits (56), Expect = 7.1
Identities = 10/48 (20%), Positives = 20/48 (41%)
Query: 61 GRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIV 108
G +A + + + E + T +G FG +LV+ + Q +
Sbjct: 155 GDIAYSGSTVKQGEAEAVVTATGMNTFFGKAAALVQSTETGSGHLQKI 202
>gnl|CDD|162007 TIGR00713, hemL, glutamate-1-semialdehyde-2,1-aminomutase. This
enzyme, glutamate-1-semialdehyde-2,1-aminomutase
(glutamate-1-semialdehyde aminotransferase, GSA
aminotransferase), contains a pyridoxal phosphate
attached at a Lys residue at position 283 of the seed
alignment. It is in the family of class III
aminotransferases.
Length = 423
Score = 25.4 bits (56), Expect = 7.6
Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 20/73 (27%)
Query: 28 PRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDI--------- 78
PR+++A+ EA G Y A E + L +A+ II+R +++
Sbjct: 67 PRVVEAVKEALERGTS-----YGAPTEAEIL----LAKE--IISRVPSVEMVRFVNSGTE 115
Query: 79 STMSGDRIAFGAT 91
+TMS R+A G T
Sbjct: 116 ATMSAVRLARGYT 128
>gnl|CDD|179965 PRK05218, PRK05218, heat shock protein 90; Provisional.
Length = 613
Score = 25.1 bits (56), Expect = 8.3
Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 7/41 (17%)
Query: 71 TRAEVID-ISTMSGDRIAFGATVSLVEKNSGD-KKNYQIVG 109
TR EVI+ + T IA T +EK GD KK+ Q++G
Sbjct: 85 TREEVIENLGT-----IAKSGTKEFLEKLKGDQKKDSQLIG 120
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 24.8 bits (54), Expect = 9.0
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 11/62 (17%)
Query: 26 ERPRIIKAISEARAYGDLSENAEYQAAK--ELQ------NLNEGR-MAELENIITRAEVI 76
E+ +I AI +AR GDL+ +E Q K EL+ EG+ M L N +T AE+
Sbjct: 480 EQAKI--AIEQARRVGDLARMSELQYGKIPELEKQLAAATQLEGKTMRLLRNKVTDAEIA 537
Query: 77 DI 78
++
Sbjct: 538 EV 539
>gnl|CDD|179811 PRK04290, PRK04290, 30S ribosomal protein S6e; Validated.
Length = 115
Score = 24.8 bits (55), Expect = 9.6
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 120 VSISSPIARALIGKELGDIISVNAPG 145
+ I A LIGK++GD I + G
Sbjct: 19 IEIDGAEANRLIGKKIGDEIDGSIVG 44
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.312 0.131 0.354
Gapped
Lambda K H
0.267 0.0697 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,541,575
Number of extensions: 152272
Number of successful extensions: 288
Number of sequences better than 10.0: 1
Number of HSP's gapped: 283
Number of HSP's successfully gapped: 43
Length of query: 158
Length of database: 5,994,473
Length adjustment: 86
Effective length of query: 72
Effective length of database: 4,136,185
Effective search space: 297805320
Effective search space used: 297805320
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 (24.3 bits)