RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6224
(82 letters)
>gnl|CDD|236179 PRK08188, PRK08188, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 714
Score = 28.5 bits (64), Expect = 0.28
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 19 HHPDIFHQGDTPREDRD 35
HHPDI DT RE+ D
Sbjct: 262 HHPDILRFLDTKRENAD 278
>gnl|CDD|131490 TIGR02437, FadB, fatty oxidation complex, alpha subunit FadB.
Members represent alpha subunit of multifunctional
enzyme complex of the fatty acid degradation cycle.
Activities include: enoyl-CoA hydratase (EC 4.2.1.17),
dodecenoyl-CoA delta-isomerase activity (EC 5.3.3.8),
3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35),
3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A
representative is E. coli FadB. This model excludes the
FadJ family represented by SP:P77399 [Fatty acid and
phospholipid metabolism, Degradation].
Length = 714
Score = 28.3 bits (63), Expect = 0.41
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 4/45 (8%)
Query: 3 GWG---SFLFAVIGVNAAHHHPDIFHQGDTPREDRDWGINQIDAV 44
GW ++L V+G++ HH + +G R +D G + IDA+
Sbjct: 532 GWPMGPAYLLDVVGIDTGHHAQAVMAEGFPDRMGKD-GRDAIDAL 575
>gnl|CDD|107297 cd06302, PBP1_LsrB_Quorum_Sensing, Periplasmic binding domain of
autoinducer-2 (AI-2) receptor LsrB from Salmonella
typhimurium and its close homologs. Periplasmic binding
domain of autoinducer-2 (AI-2) receptor LsrB from
Salmonella typhimurium and its close homologs from other
bacteria. The members of this group are homologous to a
family of periplasmic pentose/hexose sugar-binding
proteins that function as the primary receptors for
chemotaxis and transporters of many sugar based solutes
in bacteria and archaea and that are a member of the
type I periplasmic binding protein superfamily. LsrB
binds a chemically distinct form of the AI-2 signal that
lacks boron, in contrast to the Vibrio harveyi AI-2
signaling molecule that has an unusual furanosyl borate
diester. Hence, many bacteria coordinate their gene
expression according to the local density of their
population by producing species specific AI-2. This
process of quorum sensing allows LsrB to function as a
periplasmic AI-2 binding protein in interspecies
signaling.
Length = 298
Score = 27.9 bits (63), Expect = 0.49
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 25 HQGDTPREDRDWGINQIDA 43
H D ++RD+ I Q D
Sbjct: 87 HDSDVQPDNRDYDIEQADN 105
>gnl|CDD|215275 PLN02498, PLN02498, omega-3 fatty acid desaturase.
Length = 450
Score = 27.5 bits (61), Expect = 0.82
Identities = 12/22 (54%), Positives = 13/22 (59%)
Query: 61 GEHTLHHLFPTIDHCFLHIAHE 82
G H +HHLFP I H L A E
Sbjct: 370 GTHVIHHLFPQIPHYHLVEATE 391
>gnl|CDD|180738 PRK06871, PRK06871, DNA polymerase III subunit delta'; Validated.
Length = 325
Score = 27.0 bits (60), Expect = 0.92
Identities = 8/29 (27%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 16 AAHHHPDIFHQGDTPREDRDWGINQIDAV 44
A +HPD P +++D G++Q+ +
Sbjct: 69 QAGNHPDFHIL--EPIDNKDIGVDQVREI 95
>gnl|CDD|149935 pfam09039, HTH_Tnp_Mu_2, Mu DNA binding, I gamma subdomain.
Members of this family are responsible for binding the
DNA attachment sites at each end of the Mu genome. They
adopt a secondary structure comprising a four helix
bundle tightly packed around a hydrophobic core
consisting of aliphatic and aromatic amino acid
residues. Helices 1 and 2 are oriented antiparallel to
each other. Helix 3 crosses helices 1 and 2 at angles of
60 and 120 degrees, respectively. Excluding the
C-terminal helix 4, the fold of the I-gamma subdomain is
remarkably similar to that of the homeodomain family of
helix-turn-helix DNA-binding proteins, although their
amino acid sequences are completely unrelated.
Length = 108
Score = 26.4 bits (58), Expect = 1.2
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 32 EDRDWGINQIDAVRSRPDER--NQFIVLTTFGEHTLHHLFPT 71
++ W I + +++ R +VLT GEH L L+P
Sbjct: 63 QENGWTIPSLASLKRRFKAAVPETTVVLTREGEHALFKLYPA 104
>gnl|CDD|234365 TIGR03817, DECH_helic, helicase/secretion neighborhood putative
DEAH-box helicase. A conserved gene neighborhood widely
spread in the Actinobacteria contains this
uncharacterized DEAH-box family helicase encoded
convergently towards an operon of genes for protein
homologous to type II secretion and pilus formation
proteins. The context suggests that this helicase may
play a role in conjugal transfer of DNA.
Length = 742
Score = 27.0 bits (60), Expect = 1.2
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 25 HQGDTPREDRDWGINQIDAVRSRPD 49
+ GDTP E+R W V + PD
Sbjct: 114 YDGDTPTEERRWAREHARYVLTNPD 138
>gnl|CDD|235952 PRK07187, PRK07187, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 721
Score = 27.0 bits (60), Expect = 1.2
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 19 HHPDIFHQGDTPREDRD 35
HHPD+ DT RE+ D
Sbjct: 254 HHPDVLTFLDTKRENAD 270
>gnl|CDD|224759 COG1846, MarR, Transcriptional regulators [Transcription].
Length = 126
Score = 26.0 bits (57), Expect = 1.7
Identities = 11/38 (28%), Positives = 14/38 (36%)
Query: 33 DRDWGINQIDAVRSRPDERNQFIVLTTFGEHTLHHLFP 70
R I+ +R D R + LT G L L P
Sbjct: 58 KRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQLLP 95
>gnl|CDD|215943 pfam00487, FA_desaturase, Fatty acid desaturase.
Length = 251
Score = 26.1 bits (57), Expect = 1.9
Identities = 11/58 (18%), Positives = 17/58 (29%)
Query: 25 HQGDTPREDRDWGINQIDAVRSRPDERNQFIVLTTFGEHTLHHLFPTIDHCFLHIAHE 82
H G +R + + + + H HHLFP + L H
Sbjct: 177 HYGLDTEPERAARTWYERQLVTTSNSWVLNWLTGNLNYHIEHHLFPGVPWYRLPELHR 234
>gnl|CDD|106974 PHA00665, PHA00665, major capsid protein.
Length = 329
Score = 25.6 bits (56), Expect = 2.8
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 39 NQIDAVRSRPDERNQFIVLTTFGEHTLHHLFP 70
N IDA + D N I L +G +TLH ++P
Sbjct: 158 NIIDAGGTGSD--NASIWLVVWGPNTLHTIYP 187
>gnl|CDD|234112 TIGR03115, cas_csf2, CRISPR type AFERR-associated protein Csf2.
Members of this family show up near CRISPR repeats in
Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp.
EbN1, and Rhodoferax ferrireducens DSM 15236. In the
latter two species, the CRISPR/cas locus is found on a
plasmid. This family is one of several characteristic of
a type of CRISPR-associated (cas) gene cluster we
designate Aferr after A. ferrooxidans, where it is both
chromosomal and the only type of cas gene cluster found.
The gene is designated csf2 (CRISPR/cas Subtype as in A.
ferrooxidans protein 2), as it lies second closest to
the repeats [Mobile and extrachromosomal element
functions, Other].
Length = 344
Score = 25.3 bits (55), Expect = 3.6
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 3 GWGSFLFAVIGVNAAHHHPDIFHQGDTPRED 33
G+G F A++ + H D FH G ED
Sbjct: 288 GFGRFTAAILLTSDGDEHQDAFHDGRLNGED 318
>gnl|CDD|187837 cd09706, Csf2_U, CRISPR/Cas system-associated RAMP superfamily
protein Csf2. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
RAMP superfamily protein; Contains several motifs
similar to Cas7 family.
Length = 328
Score = 25.3 bits (55), Expect = 3.9
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 3 GWGSFLFAVIGVNAAHHHPDIFHQGDTPRED 33
G+G F A++ + H D FH G ED
Sbjct: 288 GFGRFTAAILLTSDGDEHQDAFHDGRLNGED 318
>gnl|CDD|234190 TIGR03376, glycerol3P_DH, glycerol-3-phosphate dehydrogenase
(NAD(+)). Members of this protein family are the
eukaryotic enzyme, glycerol-3-phosphate dehydrogenase
(NAD(+)) (EC 1.1.1.8). Enzymatic activity for 1.1.1.8
is defined as sn-glycerol 3-phosphate + NAD(+) =
glycerone phosphate + NADH. Note the very similar
reactions of enzymes defined as EC 1.1.1.94 and
1.1.99.5, assigned to families of proteins in the
bacteria.
Length = 342
Score = 25.4 bits (56), Expect = 3.9
Identities = 6/23 (26%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 4 WGSFLFAVIGVNAAHHHPDIFHQ 26
WG+ + ++ NA P++F +
Sbjct: 10 WGTAIAKIVAENAR-ALPELFEE 31
>gnl|CDD|184611 PRK14297, PRK14297, chaperone protein DnaJ; Provisional.
Length = 380
Score = 25.1 bits (55), Expect = 4.4
Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 16 AAHHHPDIFHQGDTPREDRDWGINQIDAVRSRPDERNQF 54
A +HPD ++G+ E++ IN+ V S P ++ Q+
Sbjct: 29 AIKYHPDK-NKGNKEAEEKFKEINEAYQVLSDPQKKAQY 66
>gnl|CDD|178121 PLN02505, PLN02505, omega-6 fatty acid desaturase.
Length = 381
Score = 25.0 bits (55), Expect = 5.0
Identities = 7/12 (58%), Positives = 8/12 (66%)
Query: 63 HTLHHLFPTIDH 74
H HHLF T+ H
Sbjct: 315 HVAHHLFSTMPH 326
>gnl|CDD|188995 cd06456, M3A_DCP, Peptidase family M3 dipeptidyl carboxypeptidase
(DCP). Peptidase family M3 dipeptidyl carboxypeptidase
(DCP; Dcp II; peptidyl dipeptidase; EC 3.4.15.5). This
metal-binding M3A family also includes oligopeptidase A
(OpdA; EC 3.4.24.70) enzyme. DCP cleaves dipeptides off
the C-termini of various peptides and proteins, the
smallest substrate being N-blocked tripeptides and
unblocked tetrapeptides. DCP from E. coli is inhibited
by the anti-hypertensive drug captopril, an inhibitor of
the mammalian angiotensin converting enzyme (ACE, also
called peptidyl dipeptidase A). Oligopeptidase A (OpdA)
may play a specific role in the degradation of signal
peptides after they are released from precursor forms of
secreted proteins. It can also cleave N-acetyl-L-Ala.
Length = 654
Score = 25.1 bits (56), Expect = 5.1
Identities = 9/21 (42%), Positives = 11/21 (52%), Gaps = 2/21 (9%)
Query: 56 VLTTFGE--HTLHHLFPTIDH 74
V T F E H LH L +D+
Sbjct: 441 VTTLFHEFGHALHGLLSDVDY 461
>gnl|CDD|119023 pfam10503, Esterase_phd, Esterase PHB depolymerase. This family of
proteins include acetyl xylan esterases (AXE), feruloyl
esterases (FAE), and poly(3-hydroxybutyrate) (PHB)
depolymerases.
Length = 226
Score = 25.0 bits (54), Expect = 5.7
Identities = 13/37 (35%), Positives = 16/37 (43%), Gaps = 6/37 (16%)
Query: 17 AHHHPDIF-----HQGDTPREDRDWGINQIDAVRSRP 48
AH HPD F H G D G + +DA+R
Sbjct: 121 AHCHPDRFAAVALHSGLALGCAAD-GASALDAMRRGL 156
>gnl|CDD|239583 cd03506, Delta6-FADS-like, The Delta6 Fatty Acid Desaturase
(Delta6-FADS)-like CD includes the integral-membrane
enzymes: delta-4, delta-5, delta-6, delta-8,
delta-8-sphingolipid, and delta-11 desaturases found in
vertebrates, higher plants, fungi, and bacteria. These
desaturases are required for the synthesis of highly
unsaturated fatty acids (HUFAs), which are mainly
esterified into phospholipids and contribute to
maintaining membrane fluidity. While HUFAs may be
required for cold tolerance in bacteria, plants and
fish, the primary role of HUFAs in mammals is cell
signaling. These enzymes are described as front-end
desaturases because they introduce a double bond between
the pre-exiting double bond and the carboxyl (front) end
of the fatty acid. Various substrates are involved, with
both acyl-coenzyme A (CoA) and acyl-lipid desaturases
present in this CD. Acyl-lipid desaturases are localized
in the membranes of cyanobacterial thylakoid, plant
endoplasmic reticulum (ER), and plastid; and acyl-CoA
desaturases are present in ER membrane. ER-bound plant
acyl-lipid desaturases and acyl-CoA desaturases require
cytochrome b5 as an electron donor. Most of the
eukaryotic desaturase domains have an adjacent
N-terminal cytochrome b5-like domain. This domain family
has extensive hydrophobic regions that would be capable
of spanning the membrane bilayer at least twice.
Comparison of sequences also reveals the existence of
three regions of conserved histidine cluster motifs that
contain the residues: HXXXH, HXX(X)HH, and Q/HXXHH.
These histidine residues are reported to be
catalytically essential and proposed to be the ligands
for the iron atoms contained within the homolog,
stearoyl CoA desaturase.
Length = 204
Score = 24.5 bits (54), Expect = 7.9
Identities = 6/16 (37%), Positives = 7/16 (43%)
Query: 63 HTLHHLFPTIDHCFLH 78
HHLFPT+
Sbjct: 174 QIEHHLFPTMPRHNYP 189
>gnl|CDD|182853 PRK10939, PRK10939, autoinducer-2 (AI-2) kinase; Provisional.
Length = 520
Score = 24.2 bits (53), Expect = 9.0
Identities = 7/10 (70%), Positives = 8/10 (80%)
Query: 17 AHHHPDIFHQ 26
AHH PDI+ Q
Sbjct: 145 AHHRPDIYRQ 154
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
0.328 0.143 0.491
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,406,536
Number of extensions: 348957
Number of successful extensions: 442
Number of sequences better than 10.0: 1
Number of HSP's gapped: 441
Number of HSP's successfully gapped: 33
Length of query: 82
Length of database: 10,937,602
Length adjustment: 51
Effective length of query: 31
Effective length of database: 8,675,548
Effective search space: 268941988
Effective search space used: 268941988
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 (21.7 bits)
S2: 53 (24.2 bits)