RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16278
(88 letters)
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 67.1 bits (163), Expect = 1e-14
Identities = 31/62 (50%), Positives = 41/62 (66%)
Query: 25 GVTYLRLDGSVVSTARHAIVTKFNSDPTIDVLLLTTQVGGLGLNLTGADTVIFVDHDWSP 84
G+ Y+RLDGS + R ++ +FN+D V LL+ + GGLGLNLTGADTVI D W+P
Sbjct: 735 GIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVILFDPWWNP 794
Query: 85 MK 86
Sbjct: 795 AV 796
>gnl|CDD|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain. The
Prosite family is restricted to DEAD/H helicases,
whereas this domain family is found in a wide variety
of helicases and helicase related proteins. It may be
that this is not an autonomously folding unit, but an
integral part of the helicase.
Length = 78
Score = 59.1 bits (144), Expect = 2e-13
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 2/64 (3%)
Query: 21 CEMPGVTYLRLDGSVVSTARHAIVTKFNSDPTIDVLLLTTQVGGLGLNLTGADTVIFVDH 80
PG+ RL G + R I+ F + + +L+ T V G G++L + VI D
Sbjct: 3 LRKPGIKVARLHGGLSQEEREEILEDFRNGKS--KVLVATDVAGRGIDLPDVNLVINYDL 60
Query: 81 DWSP 84
W+P
Sbjct: 61 PWNP 64
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 57.6 bits (140), Expect = 8e-13
Identities = 23/64 (35%), Positives = 31/64 (48%), Gaps = 2/64 (3%)
Query: 21 CEMPGVTYLRLDGSVVSTARHAIVTKFNSDPTIDVLLLTTQVGGLGLNLTGADTVIFVDH 80
+ G+ RL G + R I+ KFN+ +L+ T V GL+L G D VI D
Sbjct: 7 LKELGIKVARLHGGLSQEEREEILDKFNNGKI--KVLVATDVAERGLDLPGVDLVIIYDL 64
Query: 81 DWSP 84
WSP
Sbjct: 65 PWSP 68
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 58.7 bits (142), Expect = 1e-11
Identities = 27/65 (41%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 21 CEMPGVTYLRLDGSVVSTARHAIVTKFNSDPTID-VLLLTTQVGGLGLNLTGADTVIFVD 79
G Y R+DG+ R A + FN + V LL+T+ GGLG+NL AD VI D
Sbjct: 507 LMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLSTRAGGLGINLATADIVILYD 566
Query: 80 HDWSP 84
DW+P
Sbjct: 567 SDWNP 571
>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated
with DEXDc-, DEAD-, and DEAH-box proteins, yeast
initiation factor 4A, Ski2p, and Hepatitis C virus NS3
helicases; this domain is found in a wide variety of
helicases and helicase related proteins; may not be an
autonomously folding unit, but an integral part of the
helicase; 4 helicase superfamilies at present according
to the organization of their signature motifs; all
helicases share the ability to unwind nucleic acid
duplexes with a distinct directional polarity; they
utilize the free energy from nucleoside triphosphate
hydrolysis to fuel their translocation along DNA,
unwinding the duplex in the process.
Length = 131
Score = 50.7 bits (122), Expect = 1e-09
Identities = 19/60 (31%), Positives = 25/60 (41%), Gaps = 4/60 (6%)
Query: 26 VTYLRLDGSVVSTARHAIVTKFNSDPTIDVLLLTTQVGGLGLNLTGADTVIFVDHDWSPM 85
V L DGS R ++ F V+L+ T V G++L VI D WSP
Sbjct: 55 VAALHGDGSQ--EEREEVLKDFREGEI--VVLVATDVIARGIDLPNVSVVINYDLPWSPS 110
>gnl|CDD|225390 COG2834, LolA, Outer membrane lipoprotein-sorting protein [Cell
envelope biogenesis, outer membrane].
Length = 211
Score = 28.1 bits (63), Expect = 0.41
Identities = 14/76 (18%), Positives = 24/76 (31%), Gaps = 7/76 (9%)
Query: 13 KTSSKYTTCEMPGVTYLRLDGSVVSTARHAIVTKFNSDPTIDVLLLTTQVGGLGLNLTGA 72
KT T P + L +++ V+ + VL LT
Sbjct: 102 KTWLSEATGNTPLMLLLSNIKDLLNEY---NVSLLGTSDVAYVLELTP----KANLGNSK 154
Query: 73 DTVIFVDHDWSPMKLE 88
+I D +P++ E
Sbjct: 155 QRIIVDKEDGTPLRFE 170
>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 = 28.4 bits (64), Expect = 0.41
Identities = 23/59 (38%), Positives = 27/59 (45%), Gaps = 11/59 (18%)
Query: 36 VSTARHAIVTKFNSDPTIDVLLLTTQVGGLGLN------LTGADTVIFVDHDWSPMKLE 88
V T HA+V P VL++ +GGLGLN GA VI VD KLE
Sbjct: 150 VLTPYHAVVRAGEVKPGETVLVIG--LGGLGLNAVQIAKAMGA-AVIAVDIK--EEKLE 203
>gnl|CDD|226685 COG4232, COG4232, Thiol:disulfide interchange protein
[Posttranslational modification, protein turnover,
chaperones / Energy production and conversion].
Length = 569
Score = 27.7 bits (62), Expect = 0.67
Identities = 15/56 (26%), Positives = 19/56 (33%), Gaps = 6/56 (10%)
Query: 21 CEMPGVTYLRLDGSVVSTARHAIVTKFNSDPTIDVL------LLTTQVGGLGLNLT 70
C P L G V ++A + D LL +GGL LN T
Sbjct: 128 CYPPETRRFDLSGVVAASAAPSAPPAAEQQEGADSAATLKWSLLLAFLGGLLLNFT 183
>gnl|CDD|232942 TIGR00366, TIGR00366, TIGR00366 family protein. [Hypothetical
proteins, Conserved].
Length = 438
Score = 27.1 bits (60), Expect = 1.2
Identities = 17/44 (38%), Positives = 21/44 (47%)
Query: 36 VSTARHAIVTKFNSDPTIDVLLLTTQVGGLGLNLTGADTVIFVD 79
+S A V+K+ DP I LLLT L + LT V VD
Sbjct: 2 MSRFMTAFVSKWLPDPLIFALLLTLVTFVLVIVLTKQTPVSLVD 45
>gnl|CDD|111553 pfam02667, SCFA_trans, Short chain fatty acid transporter. This
family consists of two sequences annotated as short
chain fatty acid transporters, however, there are no
references giving details of experimental
characterisation of this function.
Length = 453
Score = 27.1 bits (60), Expect = 1.2
Identities = 17/44 (38%), Positives = 21/44 (47%)
Query: 36 VSTARHAIVTKFNSDPTIDVLLLTTQVGGLGLNLTGADTVIFVD 79
+S A V+K+ DP I LLLT L + LT V VD
Sbjct: 5 MSRFMTAFVSKWLPDPLIFALLLTLVTFVLVIVLTKQTPVSLVD 48
>gnl|CDD|237325 PRK13267, PRK13267, archaemetzincin-like protein; Reviewed.
Length = 179
Score = 26.9 bits (60), Expect = 1.2
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 25 GVTYLRLDGSVVSTAR 40
G+ Y L G+V+ST R
Sbjct: 91 GLAYPNLRGAVISTYR 106
>gnl|CDD|237635 PRK14184, PRK14184, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 286
Score = 26.7 bits (59), Expect = 1.7
Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 2/44 (4%)
Query: 17 KYTTCEMPGVTY--LRLDGSVVSTARHAIVTKFNSDPTIDVLLL 58
K CE G+ RL ++ + N+ P ID +LL
Sbjct: 52 KERACEDAGIVSEAFRLPADTTQEELEDLIAELNARPDIDGILL 95
>gnl|CDD|99876 cd06066, H2MP_NAD-link-bidir, Endopeptidases that belong to the
bidirectional NAD-linked hydrogenase group. This group
of endopeptidases are highly specific carboxyl-terminal
protease (HoxW protease) which releases a 24-amino-acid
peptide from HoxH prior to progression of subunit
assembly. These bidirectional hydrogenases are
heteropentamers encoded by the hox (hydrogen oxidation)
genes, in which complex HoxEFU shows the diaphorase
activity, and HoxYH constitutes the NiFe-hydrogenase.
Length = 139
Score = 25.6 bits (57), Expect = 3.4
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 65 LGLNLTGADTVIFVD 79
L +L GAD VIF+D
Sbjct: 43 LAEDLAGADRVIFID 57
>gnl|CDD|200042 TIGR00666, PBP4, D-alanyl-D-alanine carboxypeptidase, serine-type,
PBP4 family. In E. coli, this protein is known as
penicillin binding protein 4 (dacB). A signal sequence
is cleaved from a precursor form. The protein is
described as periplasmic in E. coli (Gram-negative) and
extracellular in Actinomadura R39 (Gram-positive).
Unlike some other proteins with similar activity, it
does not form transpeptidation. It is not essential for
viability. This family is related to class A
beta-lactamases [Cell envelope, Biosynthesis and
degradation of murein sacculus and peptidoglycan].
Length = 333
Score = 25.5 bits (56), Expect = 3.7
Identities = 14/49 (28%), Positives = 20/49 (40%), Gaps = 7/49 (14%)
Query: 43 IVTKFNSDPTIDVLLLTTQVGGL---GLNLTGA----DTVIFVDHDWSP 84
+V +F DPT+ + V L G+ DT F HD +P
Sbjct: 57 LVLRFGGDPTLKRQDIRNMVATLKKSGVTQIDGNVLVDTSAFSSHDRAP 105
>gnl|CDD|172665 PRK14177, PRK14177, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 284
Score = 25.7 bits (56), Expect = 3.8
Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 2/46 (4%)
Query: 15 SSKYTTCEMPGV--TYLRLDGSVVSTARHAIVTKFNSDPTIDVLLL 58
S K C G+ +RL + ++ K N DP +D +LL
Sbjct: 52 SMKVKACHKVGMGSEMIRLKEQTTTEELLGVIDKLNLDPNVDGILL 97
>gnl|CDD|178130 PLN02515, PLN02515, naringenin,2-oxoglutarate 3-dioxygenase.
Length = 358
Score = 25.7 bits (56), Expect = 4.0
Identities = 15/33 (45%), Positives = 17/33 (51%)
Query: 46 KFNSDPTIDVLLLTTQVGGLGLNLTGADTVIFV 78
K ++DP LLL QVGGL G T I V
Sbjct: 215 KRHTDPGTITLLLQDQVGGLQATRDGGKTWITV 247
>gnl|CDD|184556 PRK14185, PRK14185, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 293
Score = 25.6 bits (56), Expect = 4.1
Identities = 11/42 (26%), Positives = 18/42 (42%), Gaps = 2/42 (4%)
Query: 15 SSKYTTCEMPGV--TYLRLDGSVVSTARHAIVTKFNSDPTID 54
++K CE G + +R + V A V + N D +D
Sbjct: 50 ANKVKACEECGFKSSLIRYESDVTEEELLAKVRELNQDDDVD 91
>gnl|CDD|99872 cd00518, H2MP, Hydrogenase specific C-terminal endopeptidases,
also called Hydrogen Maturation Proteases (H2MP). These
enzymes belong to the peptidase family M52. Maturation
of [FeNi] hydrogenases includes formation of the nickel
metallocenter, proteolytic processing and assembly with
other subunits. Hydrogenase maturation endopeptidases
are responsible for the proteolytic processing,
liberating a short C-terminal peptide by cleaving after
a His or an Arg residue, e.g., HycI (E. coli) is
involved in processing of HypE, the large subunit of
hydrogenase 3. This cleavage is nickel dependent. This
CD also includes such hydrogenase-processing proteins
as HydD, HupW, and HoxW, as well as, proteins of the
F420-reducing hydrogenase of methanogens (e.g., FrcD).
Also included, is the Pyrococcus furiosus FrxA protein,
a bifunctional endopeptidase/ sulfhydrogenase found in
NADP-reducing hyperthermophiles.The Pyrococcus FrxA is
not related to those found in Helicobacter pylori.
Length = 139
Score = 25.2 bits (56), Expect = 4.6
Identities = 12/22 (54%), Positives = 12/22 (54%), Gaps = 4/22 (18%)
Query: 62 VGGLGLNLT----GADTVIFVD 79
G LGL L GAD VI VD
Sbjct: 37 GGTLGLELLDLLEGADRVIIVD 58
>gnl|CDD|180709 PRK06815, PRK06815, hypothetical protein; Provisional.
Length = 317
Score = 25.0 bits (55), Expect = 5.1
Identities = 6/24 (25%), Positives = 10/24 (41%)
Query: 65 LGLNLTGADTVIFVDHDWSPMKLE 88
L L G ++ S +KL+
Sbjct: 85 LAAKLAGIPVTVYAPEQASAIKLD 108
>gnl|CDD|215156 PLN02276, PLN02276, gibberellin 20-oxidase.
Length = 361
Score = 24.5 bits (54), Expect = 7.9
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 9/33 (27%)
Query: 50 DPTIDVLLLTTQVGGLGLNLTGADTVIFVDHDW 82
DPT +L QVGGL +FVD+ W
Sbjct: 230 DPTSLTILHQDQVGGLQ---------VFVDNKW 253
>gnl|CDD|225251 COG2376, DAK1, Dihydroxyacetone kinase [Carbohydrate transport and
metabolism].
Length = 323
Score = 24.5 bits (54), Expect = 8.6
Identities = 8/27 (29%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 8 EVHRPKTSSKYTTCEMPG--VTYLRLD 32
+ R + T+ +M G +T L+LD
Sbjct: 282 TIERTLVGNYMTSLDMAGFSITLLKLD 308
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
0.316 0.131 0.382
Gapped
Lambda K H
0.267 0.0781 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,097,681
Number of extensions: 308937
Number of successful extensions: 293
Number of sequences better than 10.0: 1
Number of HSP's gapped: 290
Number of HSP's successfully gapped: 23
Length of query: 88
Length of database: 10,937,602
Length adjustment: 56
Effective length of query: 32
Effective length of database: 8,453,778
Effective search space: 270520896
Effective search space used: 270520896
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 (21.6 bits)
S2: 53 (24.1 bits)