RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780482|ref|YP_003064895.1| ribonuclease P [Candidatus
Liberibacter asiaticus str. psy62]
(123 letters)
>gnl|CDD|144425 pfam00825, Ribonuclease_P, Ribonuclease P.
Length = 107
Score = 74.1 bits (183), Expect = 1e-14
Identities = 40/104 (38%), Positives = 59/104 (56%), Gaps = 5/104 (4%)
Query: 7 LKKRRQF-ALVKKGELRKGPFFSLEVLNNNNSNLLPRVGFTVTKKQGC-AVERNRMRRRL 64
LKKR++F A+ +KG F L N+ PR+G +V+KK G AV RNR++R L
Sbjct: 5 LKKRKEFQAVFRKGRRVASRHFVLYYRPNSLGY--PRLGISVSKKVGKRAVVRNRIKRLL 62
Query: 65 KEAVRLCAEGVLKHGHDYVLIAKRDALFIPFKELCNHFVERVRR 108
+EA RL + L G D V+IA++ AL F EL + +++
Sbjct: 63 REAFRLNKD-RLPPGLDIVVIARKGALEADFAELLKELEKLLKK 105
>gnl|CDD|30939 COG0594, RnpA, RNase P protein component [Translation, ribosomal
structure and biogenesis].
Length = 117
Score = 60.3 bits (146), Expect = 1e-10
Identities = 45/107 (42%), Positives = 65/107 (60%), Gaps = 5/107 (4%)
Query: 7 LKKRRQFALV-KKGELRKGPFFSLEVLNNNNSNLLPRVGFTVTKKQ-GCAVERNRMRRRL 64
LKKR++F V KKG+ R+ F + + NN PR+G TV+KK+ G AVERNR++R +
Sbjct: 7 LKKRKEFQAVFKKGKRRRNSLFFV-LYGRNNGLDHPRIGLTVSKKKVGNAVERNRIKRLI 65
Query: 65 KEAVRLCAEGVLKHGHDYVLIAKRDALFIPFKELCNHFVERVRRNKR 111
+EA RL L G D V+IA++ L + F EL + ++R KR
Sbjct: 66 REAFRL--LQHLLPGFDIVIIARKGFLELDFSELEKELSQLLKRAKR 110
>gnl|CDD|144675 pfam01168, Ala_racemase_N, Alanine racemase, N-terminal domain.
Length = 216
Score = 28.7 bits (65), Expect = 0.39
Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 13/56 (23%)
Query: 54 AVERN--RMRRRLKEAVRLCAEGVLK---HGHDYVLIAKRDALFIPFKELCNHFVE 104
A+ N +R R V+L A V+K +GH V +A+ A + F
Sbjct: 5 ALRHNIRALRERAGRPVKLMA--VVKANAYGHGAVRVARALA------AGADGFGV 52
>gnl|CDD|30783 COG0434, SgcQ, Predicted TIM-barrel enzyme [General function
prediction only].
Length = 263
Score = 27.5 bits (61), Expect = 0.92
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 51 QGCAVERNRMRRRLKEAVRLCAEGVLKHG 79
+G A E R R RL V++ A+ +KH
Sbjct: 129 EGNAAELARYRARLGSRVKVLADVHVKHA 157
>gnl|CDD|176451 cd08769, DAP_dppA_2, Peptidase M55, D-aminopeptidase
dipeptide-binding protein family. M55 Peptidase,
D-Aminopeptidase dipeptide-binding protein (dppA; DAP
dppA; EC 3.4.11.-) domain: Peptide transport systems are
found in many bacterial species and generally function
to accumulate intact peptides in the cell, where they
are hydrolyzed. The dipeptide-binding protein (dppA) of
Bacillus subtilis belongs to the dipeptide ABC transport
(dpp) operon expressed early during sporulation. It is a
binuclear zinc-dependent, D-specific aminopeptidase. The
biologically active enzyme is a homodecamer with active
sites buried in its channel. These
self-compartmentalizing proteases are characterized by a
SXDXEG motif. D-Ala-D-Ala and D-Ala-Gly-Gly are the
preferred substrates. Bacillus subtilis dppA is thought
to function as an adaptation to nutrient deficiency;
hydrolysis of its substrate releases D-Ala which can be
used subsequently as metabolic fuel. This family also
contains a number of uncharacterized putative
peptidases.
Length = 270
Score = 24.9 bits (55), Expect = 5.2
Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 3/59 (5%)
Query: 58 NRMRRRLKEAVRLCAEGVLKHGHDYVLIAKRDALF--IPFKELCNHFVERVRRNKRSYY 114
RR + E + E + + G + +++A I ++EL V V R
Sbjct: 29 KEARRLMTEELNAVLEELFESGFEEIVVADSHGRMDNIDYEELD-PRVSLVSGYPRPLS 86
>gnl|CDD|176216 cd08254, hydroxyacyl_CoA_DH, 6-hydroxycyclohex-1-ene-1-carboxyl-CoA
dehydrogenase, N-benzyl-3-pyrrolidinol dehydrogenase,
and other MDR family members. This group contains
enzymes of the zinc-dependent alcohol dehydrogenase
family, including members (aka MDR) identified as
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase and
N-benzyl-3-pyrrolidinol dehydrogenase.
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase
catalyzes the conversion of
6-Hydroxycyclohex-1-enecarbonyl-CoA and NAD+ to
6-Ketoxycyclohex-1-ene-1-carboxyl-CoA,NADH, and H+. This
group displays the characteristic catalytic and
structural zinc sites of the zinc-dependent alcohol
dehydrogenases. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 338
Score = 24.9 bits (55), Expect = 6.3
Identities = 11/50 (22%), Positives = 18/50 (36%), Gaps = 11/50 (22%)
Query: 61 RRRLKEAVRLCAEGVLKHGHDYVLIAKRDALFIPFKELCNHFVERVRRNK 110
L E + L A+G L + P E+ +ER+ + K
Sbjct: 291 PEDLPEVLDLIAKGKLD------PQVET----RPLDEI-PEVLERLHKGK 329
>gnl|CDD|176230 cd08269, Zn_ADH9, Alcohol dehydrogenases of the MDR family. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability.
Length = 312
Score = 24.6 bits (54), Expect = 6.7
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 6/44 (13%)
Query: 54 AVERNR--MRRRLKEAVRLCAEGVLK----HGHDYVLIAKRDAL 91
AVER+ ++EAV+L A+G L H++ L DA
Sbjct: 253 AVERDPRIGLEGMREAVKLIADGRLDLGSLLTHEFPLEELGDAF 296
>gnl|CDD|38059 KOG2848, KOG2848, KOG2848, 1-acyl-sn-glycerol-3-phosphate
acyltransferase [Lipid transport and metabolism].
Length = 276
Score = 24.4 bits (53), Expect = 7.6
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 5/37 (13%)
Query: 79 GHDYVLIAKRDALFIPFKELCNH-----FVERVRRNK 110
+ V+IAKR ++P L + F++R RR K
Sbjct: 111 PKNCVVIAKRSLFYVPIFGLAMYLSGVVFIDRSRREK 147
>gnl|CDD|145134 pfam01813, ATP-synt_D, ATP synthase subunit D. This is a family
of subunit D form various ATP synthases including
V-type H+ transporting and Na+ dependent. Subunit D is
suggested to be an integral part of the catalytic
sector of the V-ATPase.
Length = 194
Score = 24.1 bits (53), Expect = 9.9
Identities = 17/40 (42%), Positives = 22/40 (55%), Gaps = 10/40 (25%)
Query: 59 RMRRRLKEAVRLCAEGVLKHGHDYVLIAKRDALFIPFKEL 98
R++RRLK A R GH +L KRDAL + F+ L
Sbjct: 5 RLKRRLKLAQR---------GHK-LLKKKRDALILEFRAL 34
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
0.326 0.139 0.412
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,510,466
Number of extensions: 72212
Number of successful extensions: 216
Number of sequences better than 10.0: 1
Number of HSP's gapped: 212
Number of HSP's successfully gapped: 14
Length of query: 123
Length of database: 6,263,737
Length adjustment: 82
Effective length of query: 41
Effective length of database: 4,491,799
Effective search space: 184163759
Effective search space used: 184163759
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (23.3 bits)