RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|255764489|ref|YP_003065094.2| stationary phase survival
protein SurE [Candidatus Liberibacter asiaticus str. psy62]
(250 letters)
>gnl|CDD|30842 COG0496, SurE, Predicted acid phosphatase [General function
prediction only].
Length = 252
Score = 232 bits (593), Expect = 8e-62
Identities = 85/253 (33%), Positives = 140/253 (55%), Gaps = 5/253 (1%)
Query: 1 MRILLTNDDGIKSKGLITLENIARSISDDIWICAPEMDQSCLANSLTMSRNIACRTISKK 60
MRILLTNDDGI + G+ L R D+ + AP+ +QS ++SLT+ + R +
Sbjct: 1 MRILLTNDDGIHAPGIRALARALRE-GADVTVVAPDREQSGASHSLTLHEPLRVRQVDNG 59
Query: 61 RFAVHGTPVDCVVIALQK-MSDKKPDLILSGVNVGTNTSNHVAYSGTLAAAFEGSLQGIR 119
+AV+GTP DCV++ L + + + +PDL++SG+N G N + V YSGT+AAA E +L GI
Sbjct: 60 AYAVNGTPADCVILGLNELLKEPRPDLVVSGINAGANLGDDVIYSGTVAAAMEAALLGIP 119
Query: 120 SFALSQAYTYEN---MIPWEVSETHAPRVLRQLLKTQIPNTTLCNINFPRCSPEEVQKTV 176
+ A+S AY + +E + A ++ LL +P TL N+N P EE++
Sbjct: 120 AIAISLAYREAFGKQDVDFETAAKVARALVEALLANPLPPDTLLNVNIPNLPLEEIKGIR 179
Query: 177 VTAQGKPCFSIDAKQISTNDNMSHYCLTFGDHLKNLCEKSDAFAIQHNMISVTPITTDLT 236
VT G+ ++ ++ + +Y + G ++ E +D A++ IS+TP+ DLT
Sbjct: 180 VTRLGRRRYAEPVEERTDPRGEPYYWIGPGGLAEDAEEGTDFHAVREGYISITPLQLDLT 239
Query: 237 DYNSQQYISLSLE 249
Y + + + L+
Sbjct: 240 AYEALESLKSWLK 252
>gnl|CDD|145253 pfam01975, SurE, Survival protein SurE. E. coli cells with the
surE gene disrupted are found to survive poorly in
stationary phase. It is suggested that SurE may be
involved in stress response. Yeast also contains a
member of the family. A sequence from Yarrowia
lipolytica can complement a mutation in acid
phosphatase, suggesting that members of this family
could be phosphatases.
Length = 190
Score = 203 bits (520), Expect = 3e-53
Identities = 70/189 (37%), Positives = 110/189 (58%), Gaps = 5/189 (2%)
Query: 2 RILLTNDDGIKSKGLITLENIARSISDDIWICAPEMDQSCLANSLTMSRNIACRTI---S 58
RILLTNDDGI + G+ L +++ + + + AP+ +QS + +S+T+ R + + +
Sbjct: 1 RILLTNDDGIHAPGIRALAEALKALGE-VTVVAPDREQSGVGHSITLHRPLRVKKVDNDG 59
Query: 59 KKRFAVHGTPVDCVVIALQK-MSDKKPDLILSGVNVGTNTSNHVAYSGTLAAAFEGSLQG 117
+AV+GTP DCV + L + DKKPDL++SG+N G N V YSGT+ AA E +L G
Sbjct: 60 AGAYAVNGTPADCVKLGLNGLLDDKKPDLVVSGINHGANLGTDVLYSGTVGAAMEAALLG 119
Query: 118 IRSFALSQAYTYENMIPWEVSETHAPRVLRQLLKTQIPNTTLCNINFPRCSPEEVQKTVV 177
I S A+S A + +E + R++ +LLK +P TL N+N P P E++ V
Sbjct: 120 IPSIAVSLAGNSDEKDDFETAAKLVRRLVEKLLKNGLPPGTLLNVNIPALPPSEIKGIKV 179
Query: 178 TAQGKPCFS 186
T G+ ++
Sbjct: 180 TRLGRRRYA 188
>gnl|CDD|173804 cd07478, Peptidases_S8_CspA-like, Peptidase S8 family domain in
CspA-like proteins. GSP (germination-specific protease)
converts the spore peptidoglycan hydrolase (SleC)
precursor to an active enzyme during germination of
Clostridium perfringens S40 spores. Analysis of an
enzyme fraction of GSP showed that it was composed of a
gene cluster containing the processed forms of products
of cspA, cspB, and cspC which are positioned in a tandem
array just upstream of the 5' end of sleC. The amino
acid sequences deduced from the nucleotide sequences of
the csp genes showed significant similarity and showed a
high degree of homology with those of the catalytic
domain and the oxyanion binding region of
subtilisin-like serine proteases. Members of the
peptidases S8 and S35 clan include endopeptidases,
exopeptidases and also a tripeptidyl-peptidase. The S8
family has an Asp/His/Ser catalytic triad similar to
that found in trypsin-like proteases, but do not share
their three-dimensional structure and are not homologous
to trypsin. The S53 family contains a catalytic triad
Glu/Asp/Ser. The stability of these enzymes may be
enhanced by calcium, some members have been shown to
bind up to 4 ions via binding sites with different
affinity. Some members of this clan contain disulfide
bonds. These enzymes can be intra- and extracellular,
some function at extreme temperatures and pH values.
Length = 455
Score = 28.7 bits (65), Expect = 1.6
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 83 KPDLILSGVNVGTNTSN--HVAYSGTLAAA 110
KPD+ GVN+ T + + SGT AA
Sbjct: 374 KPDIAAPGVNILTASPGGGYTTRSGTSVAA 403
>gnl|CDD|144789 pfam01320, Colicin_Pyocin, Colicin immunity protein / pyocin
immunity protein.
Length = 85
Score = 27.2 bits (61), Expect = 4.3
Identities = 9/22 (40%), Positives = 11/22 (50%), Gaps = 3/22 (13%)
Query: 167 CSPEEVQKTVV---TAQGKPCF 185
SPE + K + A GKP F
Sbjct: 62 DSPEGIVKEIKEWRAANGKPGF 83
>gnl|CDD|107381 cd06386, PBP1_NPR_C_like, Ligand-binding domain of type C
natriuretic peptide receptor. Ligand-binding domain of
type C natriuretic peptide receptor (NPR-C). NPR-C is
found in atrial, mesentery, placenta, lung, kidney,
venous tissue, aortic smooth muscle, and aortic
endothelial cells. The affinity of NPR-C for
natriuretic peptides is ANP>CNP>BNP. The extracellular
domain of NPR-C is about 30% identical to NPR-A and
NPR-B. However, unlike the cyclase-linked receptors, it
contains only 37 intracellular amino acids and no
guanylyl cyclase activity. Major function of NPR-C is
to clear natriuretic peptides from the circulation or
extracellular surroundings through constitutive
receptor-mediated internalization and degradation.
Length = 387
Score = 27.1 bits (60), Expect = 4.9
Identities = 16/35 (45%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 61 RFAVHGTPVDCVVIALQKMSD----KKPDLILSGV 91
RF VH DC AL + D +KPDLIL V
Sbjct: 41 RFNVHYEDSDCGNEALFSLVDRSCARKPDLILGPV 75
>gnl|CDD|132725 cd06528, RNAP_A'', A'' subunit of Archaeal RNA Polymerase (RNAP).
Archaeal RNA polymerase (RNAP), like bacterial RNAP, is
a large multi-subunit complex responsible for the
synthesis of all RNAs in the cell. The relative
positioning of the RNAP core is highly conserved between
archaeal RNAP and the three classes of eukaryotic RNAPs.
In archaea, the largest subunit is split into two
polypeptides, A' and A'', which are encoded by separate
genes in an operon. Sequence alignments reveal that the
archaeal A'' subunit corresponds to the C-terminal
one-third of the RNAPII largest subunit (Rpb1). In
subunit A'', several loops in the jaw domain are
shorter. The RNAPII Rpb1 interacts with the
second-largest subunit (Rpb2) to form the DNA entry and
RNA exit channels in addition to the catalytic center of
RNA synthesis.
Length = 363
Score = 26.4 bits (59), Expect = 7.0
Identities = 20/87 (22%), Positives = 40/87 (45%), Gaps = 15/87 (17%)
Query: 18 TLENIARSISDDIWICA--PEMDQSCLANS-LTMSRNIACRTISK-KRFAVHGTPVDCVV 73
TLEN+A IS D++ E+D+ L + +T+ + I K K+ V ++
Sbjct: 121 TLENLAEDISIDLFNMRITIELDEEMLEDRGITVDDVLK--AIEKLKKGKVGEEGDVTLI 178
Query: 74 I---------ALQKMSDKKPDLILSGV 91
+ L+K+++K + + G+
Sbjct: 179 VLKAEEPSIKELRKLAEKILNTKIKGI 205
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
0.318 0.130 0.383
Gapped
Lambda K H
0.267 0.0830 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,745,954
Number of extensions: 130415
Number of successful extensions: 301
Number of sequences better than 10.0: 1
Number of HSP's gapped: 295
Number of HSP's successfully gapped: 12
Length of query: 250
Length of database: 6,263,737
Length adjustment: 91
Effective length of query: 159
Effective length of database: 4,297,318
Effective search space: 683273562
Effective search space used: 683273562
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 (21.8 bits)
S2: 56 (25.2 bits)