RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13292
(198 letters)
>gnl|CDD|220417 pfam09812, MRP-L28, Mitochondrial ribosomal protein L28. Members
of this family are components of the mitochondrial large
ribosomal subunit. Mature mitochondrial ribosomes
consist of a small (37S) and a large (54S) subunit. The
37S subunit contains at least 33 different proteins and
1 molecule of RNA (15S). The 54S subunit contains at
least 45 different proteins and 1 molecule of RNA (21S).
Length = 146
Score = 85.1 bits (211), Expect = 2e-21
Identities = 36/88 (40%), Positives = 53/88 (60%)
Query: 69 KKIRSRALPPLSEEVIESRSNLIKEWGIYRSKEAQKDYKLIDRLIYSQQRALDELRLESE 128
K R R L LS E +E R+ + K W +Y+ +E + + + + + +QQ AL+EL+LES
Sbjct: 54 AKRRQRKLLKLSPEDLERRALIEKCWALYQQQEREAENQQLRQQYEAQQEALEELKLESP 113
Query: 129 ELYQEAIQIDPTLLPFAAKGPLHTPPIE 156
ELY+ AI DP L P +GP TPP +
Sbjct: 114 ELYEAAIAPDPGLFPLELRGPTDTPPND 141
>gnl|CDD|220555 pfam10079, DUF2317, Uncharacterized protein conserved in bacteria
(DUF2317). Members of this family of hypothetical
bacterial proteins have no known function.
Length = 541
Score = 35.6 bits (83), Expect = 0.012
Identities = 21/83 (25%), Positives = 33/83 (39%), Gaps = 10/83 (12%)
Query: 65 PHQRKKIRSRALPPLSEEVIESRSNLIKEWGIYRSKEAQKDYKLIDRLIYSQQRALDELR 124
P KK+ L E+V L+KE + ++ ID + A EL
Sbjct: 386 PKVEKKLDKLGLSI--EDVFLHGLELLKEKVLEEKANSE-----IDIDF---EEAKAELE 435
Query: 125 LESEELYQEAIQIDPTLLPFAAK 147
+ + L +EA +IDP+L
Sbjct: 436 AQFKRLREEAAKIDPSLEGALEA 458
>gnl|CDD|183140 PRK11447, PRK11447, cellulose synthase subunit BcsC; Provisional.
Length = 1157
Score = 32.4 bits (74), Expect = 0.17
Identities = 13/44 (29%), Positives = 25/44 (56%), Gaps = 2/44 (4%)
Query: 95 GIYRSKEAQKDYKLIDRLIYSQQRALDELR--LESEELYQEAIQ 136
+YR + +K I L SQ+R++D++ L+++ L Q+A
Sbjct: 427 NLYRQQSPEKALAFIASLSASQRRSIDDIERSLQNDRLAQQAEA 470
>gnl|CDD|224273 COG1354, scpA, Rec8/ScpA/Scc1-like protein (kleisin family)
[Replication, recombination, and repair].
Length = 248
Score = 30.4 bits (69), Expect = 0.45
Identities = 12/65 (18%), Positives = 25/65 (38%)
Query: 50 DRKAALEEILNKNKKPHQRKKIRSRALPPLSEEVIESRSNLIKEWGIYRSKEAQKDYKLI 109
D A ++IL + K+ + R EE +E ++ G+ R + +
Sbjct: 145 DLFRAYQKILRRVKQEELVEIERIVLEELSVEEQLEELLARLEARGVLRFSDLFSPEERK 204
Query: 110 DRLIY 114
D ++
Sbjct: 205 DEVVS 209
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 30.1 bits (69), Expect = 0.69
Identities = 23/96 (23%), Positives = 46/96 (47%), Gaps = 23/96 (23%)
Query: 42 RNFEKEYRDRKAALEEILNKNKKPHQRKKIRSRALPPLSEEVIESRSNLIKEWGIYRSKE 101
FEKE R+R+ L+ K++ + EE ++ + L+++ R +E
Sbjct: 71 NEFEKELRERRNELQ---------KLEKRLLQK------EENLDRKLELLEK----REEE 111
Query: 102 AQKDYKLIDRLIYSQQRALDELRLESEELYQEAIQI 137
+K K +++ +Q+ L++ E EEL +E +Q
Sbjct: 112 LEKKEKELEQ----KQQELEKKEEELEELIEEQLQE 143
>gnl|CDD|234345 TIGR03755, conj_TIGR03755, integrating conjugative element protein,
PFL_4711 family. Members of this protein family are
found in genomic regions associated with conjugative
transfer and integrated TOL-like plasmids. The specific
function is unknown [Mobile and extrachromosomal element
functions, Plasmid functions].
Length = 418
Score = 28.4 bits (64), Expect = 2.6
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 44 FEKEYRDRKAALEEILNKNKKPHQR--KKIRSRALPPLSEEVIES 86
E+EY AL+++++ P Q K S +L P++ VIE+
Sbjct: 259 IEEEYDSNLEALQKLVSGATPPTQENLAKASSPSL-PITRGVIEA 302
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 28.3 bits (64), Expect = 2.8
Identities = 28/124 (22%), Positives = 48/124 (38%), Gaps = 18/124 (14%)
Query: 81 EEVIESRSNLIKEWGIYRS------KEAQKDYKLIDRLIYSQQRALDELRLESEELYQEA 134
E+I S L +E KEA+K + ++ Q D+L E+E+ Q+A
Sbjct: 519 NELIASLEELERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQA 578
Query: 135 IQIDPTLLPFAAKGPLHTPPIENYECPDGDYTDVSRNFEKEYRDRKAALEEILNKNKKPH 194
I+ AK E + G Y V E + + L + N+ K+
Sbjct: 579 IK--------EAKKEADEIIKELRQLQKGGYASVK---AHELIEARKRLNKA-NEKKEKK 626
Query: 195 QRKK 198
++K+
Sbjct: 627 KKKQ 630
>gnl|CDD|185262 PRK15364, PRK15364, pathogenicity island 2 effector protein SseB;
Provisional.
Length = 196
Score = 27.7 bits (61), Expect = 3.9
Identities = 17/55 (30%), Positives = 26/55 (47%)
Query: 52 KAALEEILNKNKKPHQRKKIRSRALPPLSEEVIESRSNLIKEWGIYRSKEAQKDY 106
KAAL+ N+N + +I + + V+ + LI +WG S AQK Y
Sbjct: 141 KAALDNDANRNTDLMSQGQITIQKMSQELNAVLTQLTGLISKWGEISSMIAQKTY 195
>gnl|CDD|224706 COG1793, CDC9, ATP-dependent DNA ligase [DNA replication,
recombination, and repair].
Length = 444
Score = 27.7 bits (62), Expect = 4.3
Identities = 7/29 (24%), Positives = 14/29 (48%)
Query: 44 FEKEYRDRKAALEEILNKNKKPHQRKKIR 72
+R+A LEE++ + K ++I
Sbjct: 240 RGLPLEERRALLEELVKSSDKIEIAERIP 268
Score = 27.0 bits (60), Expect = 8.3
Identities = 6/21 (28%), Positives = 11/21 (52%)
Query: 172 FEKEYRDRKAALEEILNKNKK 192
+R+A LEE++ + K
Sbjct: 240 RGLPLEERRALLEELVKSSDK 260
>gnl|CDD|183698 PRK12715, flgK, flagellar hook-associated protein FlgK;
Provisional.
Length = 649
Score = 27.8 bits (61), Expect = 4.7
Identities = 14/53 (26%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 106 YKLIDRLIYSQQRALDELRLESEELYQEAIQIDPTLLPFAAKGPLHTPPIENY 158
Y+ +D+ +Q R+ R + + Y +AIQID L + G + P++ +
Sbjct: 63 YRNVDQFANAQVRSTLSYRTQYDAFYNQAIQIDKLL---SQDGSSISVPLQTF 112
>gnl|CDD|236517 PRK09440, avtA, valine--pyruvate transaminase; Provisional.
Length = 416
Score = 27.5 bits (62), Expect = 5.4
Identities = 23/76 (30%), Positives = 29/76 (38%), Gaps = 23/76 (30%)
Query: 71 IRSRALPPLSEEVIESRSNLIKEWGIYRSKEAQKDYKLIDR-------LIYSQQRA---- 119
I S L LSE VI YR K Q L+ R LI+ + A
Sbjct: 293 IESGDLLRLSETVIRPF---------YRQK-VQLAIALLRRYLPDEPCLIHKPEGAIFLW 342
Query: 120 --LDELRLESEELYQE 133
+L + +EELYQ
Sbjct: 343 LWFKDLPITTEELYQR 358
>gnl|CDD|213961 TIGR04348, TIGR04348, putative glycosyltransferase, TIGR04348
family. This putative glycosyltransferase is found in
marine bacteria such as Marinobacter and soil bacteria
such as Anaeromyxobacter, but does not seem to occur in
known pathogenic bacteria.
Length = 310
Score = 26.9 bits (60), Expect = 6.5
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 4/49 (8%)
Query: 96 IYRSKEAQKDYKLIDRLIYSQQRALDEL----RLESEELYQEAIQIDPT 140
I+ EAQ+ +L DRL+ Q R LD L R ++ +YQ A P
Sbjct: 83 IHTDPEAQRSLELADRLVVLQDRGLDALPPALRAKARVIYQSAPARRPR 131
>gnl|CDD|234437 TIGR03998, thiol_BshC, bacillithiol biosynthesis cysteine-adding
enzyme BshC. Members of this protein family are BshC,
an enzyme required for bacillithiol biosynthesis and
described as a cysteine-adding enzyme. Bacillithiol is a
low-molecular-weight thiol, an analog of glutathione and
mycothiol, and is found largely in the Firmicutes
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Glutathione and analogs].
Length = 528
Score = 26.9 bits (60), Expect = 8.7
Identities = 16/83 (19%), Positives = 31/83 (37%), Gaps = 11/83 (13%)
Query: 65 PHQRKKIRSRALPPLSEEVIESRSNLIKEWGIYRSKEAQKDYKLIDRLIYSQQRALDELR 124
P K + L ++ L + + ++ + ID L + A +++
Sbjct: 377 PRVEKLLDKYQLSV--ADIFTGVEGLKERF---LERQDPEP---IDALF---EEAKEQIT 425
Query: 125 LESEELYQEAIQIDPTLLPFAAK 147
+ L +E +DPTL A K
Sbjct: 426 AAHKPLREELAAVDPTLQGLAEK 448
>gnl|CDD|135898 PRK06397, PRK06397, V-type ATP synthase subunit H; Validated.
Length = 111
Score = 25.7 bits (56), Expect = 8.7
Identities = 16/56 (28%), Positives = 24/56 (42%), Gaps = 3/56 (5%)
Query: 81 EEVIESRSNLIKEWGIYRSKEAQKDYKLIDRLIYSQQRALDELRLESEELYQEAIQ 136
+ + N IKE +SK +K K + + AL E R E+E+ E I
Sbjct: 27 ANIKNEQENEIKE---AKSKYEEKAKKTEEESLNMYNAALMEARKEAEKKAVEIIN 79
>gnl|CDD|206672 cd01885, EF2, Elongation Factor 2 (EF2) in archaea and eukarya.
Translocation requires hydrolysis of a molecule of GTP
and is mediated by EF-G in bacteria and by eEF2 in
eukaryotes. The eukaryotic elongation factor eEF2 is a
GTPase involved in the translocation of the
peptidyl-tRNA from the A site to the P site on the
ribosome. The 95-kDa protein is highly conserved, with
60% amino acid sequence identity between the human and
yeast proteins. Two major mechanisms are known to
regulate protein elongation and both involve eEF2.
First, eEF2 can be modulated by reversible
phosphorylation. Increased levels of phosphorylated eEF2
reduce elongation rates presumably because
phosphorylated eEF2 fails to bind the ribosomes.
Treatment of mammalian cells with agents that raise the
cytoplasmic Ca2+ and cAMP levels reduce elongation rates
by activating the kinase responsible for phosphorylating
eEF2. In contrast, treatment of cells with insulin
increases elongation rates by promoting eEF2
dephosphorylation. Second, the protein can be
post-translationally modified by ADP-ribosylation.
Various bacterial toxins perform this reaction after
modification of a specific histidine residue to
diphthamide, but there is evidence for endogenous ADP
ribosylase activity. Similar to the bacterial toxins, it
is presumed that modification by the endogenous enzyme
also inhibits eEF2 activity.
Length = 218
Score = 26.4 bits (59), Expect = 9.5
Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 7/29 (24%)
Query: 109 IDRLIYSQQRALDELRLESEELYQEAIQI 137
IDRLI EL+L EE YQ ++I
Sbjct: 134 IDRLIL-------ELKLSPEEAYQRLLRI 155
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.313 0.134 0.387
Gapped
Lambda K H
0.267 0.0778 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,628,106
Number of extensions: 1023987
Number of successful extensions: 1074
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1065
Number of HSP's successfully gapped: 64
Length of query: 198
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 106
Effective length of database: 6,857,034
Effective search space: 726845604
Effective search space used: 726845604
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: 56 (25.3 bits)