RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780440|ref|YP_003064853.1| transcription elongation
factor GreA [Candidatus Liberibacter asiaticus str. psy62]
(158 letters)
>gnl|CDD|31125 COG0782, GreA, Transcription elongation factor [Transcription].
Length = 151
Score = 146 bits (369), Expect = 3e-36
Identities = 70/152 (46%), Positives = 101/152 (66%), Gaps = 1/152 (0%)
Query: 7 VTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAEL 66
+T +GF K+++EL + + ERP I++ I++AR GDLSENAEY+AAKE Q E R+ L
Sbjct: 1 LTDEGFRKLKEELEYLKPVERPEIVEEIADARELGDLSENAEYRAAKEEQAFIERRIRLL 60
Query: 67 ENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPI 126
E ++ A+VID D + FG+TV+L + G++ Y IVG EAD G +S+ SP+
Sbjct: 61 EELLRNAQVIDDEKPP-DVVTFGSTVTLENLDDGEEVTYTIVGPDEADPAKGKISVDSPL 119
Query: 127 ARALIGKELGDIISVNAPGGEKTYEILQVLWI 158
RAL+GK++GD + VN PGGEK EIL + +
Sbjct: 120 GRALLGKKVGDTVEVNTPGGEKEVEILSIEYQ 151
>gnl|CDD|146205 pfam03449, GreA_GreB_N, domain. This domain adopts a long
alpha-hairpin structure.
Length = 71
Score = 96.4 bits (241), Expect = 3e-21
Identities = 40/71 (56%), Positives = 53/71 (74%)
Query: 5 IPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMA 64
P+T +G++K+Q+EL + ERP IIKAI+EAR +GDLSENAEY AAKE Q E R+
Sbjct: 1 NPITPEGYEKLQEELERLKNVERPEIIKAIAEAREHGDLSENAEYHAAKEEQREIEARIR 60
Query: 65 ELENIITRAEV 75
ELE+ + RAE+
Sbjct: 61 ELEDRLARAEI 71
>gnl|CDD|144753 pfam01272, GreA_GreB, Transcription elongation factor, GreA/GreB,
C-term. This domain has a FKBP-like fold.
Length = 77
Score = 95.3 bits (238), Expect = 7e-21
Identities = 35/75 (46%), Positives = 53/75 (70%)
Query: 81 MSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIIS 140
+ D + FG+TV+L + + G+++ Y IVG EAD G +S+ SP+ RAL+GK++GD +
Sbjct: 1 LPADVVTFGSTVTLEDLDDGEEETYTIVGPDEADPSKGKISVLSPLGRALLGKKVGDEVE 60
Query: 141 VNAPGGEKTYEILQV 155
V AP GEK YEIL++
Sbjct: 61 VTAPSGEKKYEILKI 75
>gnl|CDD|143439 cd07121, ALDH_EutE, Ethanolamine utilization protein EutE-like.
Coenzyme A acylating aldehyde dehydrogenase (ACDH), an
NAD+ and CoA-dependent acetaldehyde dehydrogenase,
acetylating (EC=1.2.1.10), converts acetaldehyde into
acetyl-CoA. This CD is limited to such monofunctional
enzymes as the Ethanolamine utilization protein, EutE,
in Salmonella typhimurium. Mutations in eutE abolish
the ability to utilize ethanolamine as a carbon source.
Length = 429
Score = 28.0 bits (63), Expect = 1.3
Identities = 21/77 (27%), Positives = 33/77 (42%), Gaps = 12/77 (15%)
Query: 16 QQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGR----MAELENIIT 71
Q++ R +R +II+AI EA L NAE A ++ GR +A+
Sbjct: 17 QKQYRKCTLADREKIIEAIREA-----LLSNAEELAEMAVEETGMGRVEDKIAKNHLAAE 71
Query: 72 RA---EVIDISTMSGDR 85
+ E + + SGD
Sbjct: 72 KTPGTEDLTTTAWSGDN 88
>gnl|CDD|147187 pfam04890, DUF648, Family of unknown function (DUF648). Family
of hypothetical Chlamydia proteins. This family may
well comprise of two domains, as some members only
match the N-terminus.
Length = 288
Score = 27.1 bits (60), Expect = 2.1
Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 3/30 (10%)
Query: 71 TRAEVIDISTMSGDRIAF---GATVSLVEK 97
R +VI +ST +G RIA G +VS EK
Sbjct: 31 KRTKVISLSTENGLRIAAKQEGVSVSTTEK 60
>gnl|CDD|112956 pfam04166, PdxA, Pyridoxal phosphate biosynthetic protein PdxA. In
Escherichia coli the coenzyme pyridoxal 5'-phosphate is
synthesized de novo by a pathway that is thought to
involve the condensation of
4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose,
catalysed by the enzymes PdxA and PdxJ, to form either
pyridoxine (vitamin B6) or pyridoxine 5'-phosphate.
Length = 299
Score = 26.2 bits (58), Expect = 4.4
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 25 EERPRIIKAISEARAYG 41
EE II A+ +ARA G
Sbjct: 198 EEIEEIIPALEQARAEG 214
>gnl|CDD|146701 pfam04199, Cyclase, Putative cyclase. Proteins in this family
are thought to be cyclase enzymes. They are found in
proteins involved in antibiotic synthesis. However they
are also found in organisms that do not make
antibiotics pointing to a wider role for these
proteins. The proteins contain a conserved motif
HXGTHXDXPXH that is likely to form part of the active
site.
Length = 162
Score = 25.8 bits (57), Expect = 5.7
Identities = 3/20 (15%), Positives = 8/20 (40%)
Query: 65 ELENIITRAEVIDISTMSGD 84
LE + ++D++
Sbjct: 69 PLEWFVGPGVLLDVAHKLPP 88
>gnl|CDD|99711 cd05828, Sortase_D_4, Sortase D (SrtD) is a membrane transpeptidase
found in gram-positive bacteria that anchors surface
proteins to peptidoglycans of the bacterial cell wall
envelope. This involves a transpeptidation reaction in
which the surface protein substrate is cleaved at the
cell wall sorting signal and covalently linked to
peptidoglycan for display on the bacterial surface.
Sortases are grouped into different classes and
subfamilies based on sequence, membrane topology,
genomic positioning, and cleavage site preference. Class
D sortases are further classified into subfamilies 4 and
5. This group contains a subset of Class D sortases
belonging to subfamily-4. These sortases recognize a
unique sorting signal (LPXTA) and they constitute a
specialized sorting pathway found in bacilli. Their
substrates are predicted to be predominantly enzymes
such as 5'-nucleotidases, glycosyl hydrolase, and
subtilase..
Length = 127
Score = 25.6 bits (57), Expect = 6.0
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 134 ELGDIISVNAPGGEKTYEI 152
E GDII++ GG TY +
Sbjct: 63 EPGDIITLQTLGGTYTYRV 81
>gnl|CDD|37834 KOG2623, KOG2623, KOG2623, Tyrosyl-tRNA synthetase [Translation,
ribosomal structure and biogenesis].
Length = 467
Score = 25.7 bits (56), Expect = 6.2
Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 1/46 (2%)
Query: 57 NLNEGRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDK 102
G + NI ++I M FG T L+ ++G K
Sbjct: 229 RFQLGGSDQWGNITAGTDLIR-KIMPIQAFVFGLTFPLLTSSTGAK 273
>gnl|CDD|145100 pfam01765, RRF, Ribosome recycling factor. The ribosome recycling
factor (RRF / ribosome release factor) dissociates the
ribosome from the mRNA after termination of translation,
and is essential bacterial growth. Thus ribosomes are
"recycled" and ready for another round of protein
synthesis.
Length = 165
Score = 25.2 bits (56), Expect = 7.5
Identities = 9/48 (18%), Positives = 24/48 (50%)
Query: 27 RPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAE 74
R + + ++SE+ +A KE+Q L + + +++ ++ + E
Sbjct: 114 RRDANDKLKKLEKDKEISEDEVKKAEKEIQKLTDKYIKKIDELLKKKE 161
>gnl|CDD|36896 KOG1683, KOG1683, KOG1683, Hydroxyacyl-CoA dehydrogenase/enoyl-CoA
hydratase [Lipid transport and metabolism].
Length = 380
Score = 25.3 bits (55), Expect = 7.5
Identities = 12/82 (14%), Positives = 26/82 (31%), Gaps = 12/82 (14%)
Query: 8 TSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNL------NEG 61
T KG + L ++ +R + + + + ++ NE
Sbjct: 255 TGKGIYPYARGLT--KKMKRDEMEALLRRLSLTPNPRVADD----EDFVEFLLSPFVNEA 308
Query: 62 RMAELENIITRAEVIDISTMSG 83
LE + DI+++ G
Sbjct: 309 LRCLLEGLKASPSDGDIASVFG 330
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.312 0.131 0.354
Gapped
Lambda K H
0.267 0.0721 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,740,163
Number of extensions: 80299
Number of successful extensions: 175
Number of sequences better than 10.0: 1
Number of HSP's gapped: 174
Number of HSP's successfully gapped: 25
Length of query: 158
Length of database: 6,263,737
Length adjustment: 86
Effective length of query: 72
Effective length of database: 4,405,363
Effective search space: 317186136
Effective search space used: 317186136
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 (24.2 bits)