RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8407
(92 letters)
>gnl|CDD|226005 COG3474, COG3474, Cytochrome c2 [Energy production and conversion].
Length = 135
Score = 144 bits (366), Expect = 1e-46
Identities = 52/93 (55%), Positives = 65/93 (69%), Gaps = 2/93 (2%)
Query: 2 KCAQCHTIEAGGAHKVGPNLHGLIGRKTGQAPGFSYTEANIKK--GITWNKDTLFEYLEN 59
KC CH+IE GG +KVGP+L G++GR G GFSY+ A K GI W++D L E+L
Sbjct: 40 KCQACHSIEKGGPNKVGPHLWGVVGRPAGSVEGFSYSAAMKKAGGGIVWDEDNLDEFLTA 99
Query: 60 PKKYIPGTKMIFAGIKKPQERGDLIAYLEQASK 92
PKKY+PGTKM FAG+KK Q+R DLIAYL+
Sbjct: 100 PKKYVPGTKMAFAGLKKDQDRADLIAYLKSLPS 132
>gnl|CDD|185414 PTZ00048, PTZ00048, cytochrome c; Provisional.
Length = 115
Score = 135 bits (342), Expect = 4e-43
Identities = 60/91 (65%), Positives = 69/91 (75%), Gaps = 1/91 (1%)
Query: 2 KCAQCHTIEAGGAHKVGPNLHGLIGRKTGQAPGFSYTEANIKKGITWNKDTLFEYLENPK 61
KCAQCHTI GGA K GPNLHG GRK+G + F Y++AN GI W+ LFEYL NPK
Sbjct: 25 KCAQCHTINKGGAVKQGPNLHGFYGRKSG-SADFPYSDANKNSGIVWSDKHLFEYLVNPK 83
Query: 62 KYIPGTKMIFAGIKKPQERGDLIAYLEQASK 92
YIPGTKM+FAGIKK +ER DLIAYL++AS
Sbjct: 84 LYIPGTKMVFAGIKKEKERADLIAYLKEASS 114
>gnl|CDD|173596 PTZ00405, PTZ00405, cytochrome c; Provisional.
Length = 114
Score = 117 bits (294), Expect = 6e-36
Identities = 52/87 (59%), Positives = 66/87 (75%)
Query: 2 KCAQCHTIEAGGAHKVGPNLHGLIGRKTGQAPGFSYTEANIKKGITWNKDTLFEYLENPK 61
+ AQCHT GG++ VGPNL G++ RK+G GF+Y++AN G+ W + L YLENPK
Sbjct: 24 RAAQCHTATKGGSNGVGPNLFGIVNRKSGTVEGFAYSKANADSGVIWTPEVLDVYLENPK 83
Query: 62 KYIPGTKMIFAGIKKPQERGDLIAYLE 88
K++PGTKM FAGIKKPQER D+IAYLE
Sbjct: 84 KFMPGTKMSFAGIKKPQERADVIAYLE 110
>gnl|CDD|215669 pfam00034, Cytochrom_C, Cytochrome c. The Pfam entry does not
include all Prosite members. The cytochrome 556 and
cytochrome c' families are not included. All these are
now in a new clan together. The C-terminus of DUF989,
pfam06181, has now been merged into this family.
Length = 81
Score = 36.8 bits (85), Expect = 1e-04
Identities = 18/87 (20%), Positives = 22/87 (25%), Gaps = 17/87 (19%)
Query: 1 MKCAQCHTIEAGGAHKVGPNLHGLIGRKTGQAPGFSYTEANIKKGITWNKDTLFEYLENP 60
CA CH + GA GP L G A + A
Sbjct: 8 ANCAACHGADGKGAGG-GPALAGAPAGYLLDALAAIKSGARGIGAQAV------------ 54
Query: 61 KKYIPGTKMIFAGIKKPQERGDLIAYL 87
A +ER L AY+
Sbjct: 55 ----MSKAPGNATQLTDEERAALAAYI 77
>gnl|CDD|205620 pfam13442, Cytochrome_CBB3, Cytochrome C oxidase, cbb3-type,
subunit III.
Length = 67
Score = 30.0 bits (68), Expect = 0.033
Identities = 21/85 (24%), Positives = 26/85 (30%), Gaps = 31/85 (36%)
Query: 3 CAQCHTIEAGGAHKVGPNLHGLIGRKTGQAPGFSYTEANIKKGITWNKDTLFEYLENPKK 62
CA CH GG GP L G + L + + N K
Sbjct: 14 CAACHG--TGG---AGPPLF----------------------GDALAPEALIKIVLNGKG 46
Query: 63 YIPGTKMIFAGIKKPQERGDLIAYL 87
+P F G +E L AYL
Sbjct: 47 AMPA----FGGDLSDEEIEALAAYL 67
>gnl|CDD|129864 TIGR00782, ccoP, cytochrome c oxidase, cbb3-type, subunit III.
This model describes a di-heme subunit of approximately
26 kDa of the cbb3 type copper and heme-containing
cytochrome oxidase [Energy metabolism, Electron
transport].
Length = 285
Score = 27.9 bits (62), Expect = 0.59
Identities = 22/58 (37%), Positives = 22/58 (37%), Gaps = 4/58 (6%)
Query: 3 CAQCHTIEAGGAHKVGPNLHGLIGRKTGQAPGFSYTEANIKKGITWNKDTLFEYLENP 60
CAQCH AGGA PNL G G T IK GI D E P
Sbjct: 118 CAQCHGSGAGGAKGF-PNLLDNDWLWGGTLEGIHTT---IKHGIRDPDDGDTYVGEMP 171
>gnl|CDD|236551 PRK09533, PRK09533, bifunctional transaldolase/phosoglucose
isomerase; Validated.
Length = 948
Score = 26.9 bits (60), Expect = 1.5
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 64 IPGTKMIFAGIKKPQERGD 82
+PG K F +K Q RGD
Sbjct: 894 VPGQKYSFGVVKAAQARGD 912
>gnl|CDD|226818 COG4383, COG4383, Mu-like prophage protein gp29 [Function
unknown].
Length = 517
Score = 26.7 bits (59), Expect = 2.0
Identities = 14/39 (35%), Positives = 17/39 (43%), Gaps = 2/39 (5%)
Query: 53 LFEYLENPKKYIPGTKMIFAGIKKPQERGDLIAYLEQAS 91
Y E+P I K A I + ERGDL A E +
Sbjct: 27 TRVYAEHPSSGITPQKA--AAILEAAERGDLRAQSELFA 63
>gnl|CDD|219475 pfam07583, PSCyt2, Protein of unknown function (DUF1549). A family
of paralogues in the planctomyces.
Length = 200
Score = 26.4 bits (59), Expect = 2.0
Identities = 8/19 (42%), Positives = 9/19 (47%), Gaps = 6/19 (31%)
Query: 1 MKCAQCHTIEAGGAHKVGP 19
+ CAQCH HK P
Sbjct: 166 LGCAQCHD------HKFDP 178
>gnl|CDD|224921 COG2010, CccA, Cytochrome c, mono- and diheme variants [Energy
production and conversion].
Length = 150
Score = 26.1 bits (57), Expect = 2.6
Identities = 10/21 (47%), Positives = 10/21 (47%), Gaps = 2/21 (9%)
Query: 3 CAQCHTIEAGGA--HKVGPNL 21
CA CH GGA GP L
Sbjct: 62 CAACHGPNLGGAGPLLDGPAL 82
>gnl|CDD|220265 pfam09491, RE_AlwI, AlwI restriction endonuclease. This family
includes the AlwI (recognises GGATC), Bsp6I (recognises
GC^NGC), BstNBI (recognises GASTC), PleI(recognises
GAGTC) and MlyI (recognises GAGTC) restriction
endonucleases.
Length = 429
Score = 26.2 bits (58), Expect = 2.7
Identities = 10/58 (17%), Positives = 25/58 (43%), Gaps = 5/58 (8%)
Query: 35 FSYTEANIKKGITWNKDTLFEYLENPKKYIPGTKMIFA-----GIKKPQERGDLIAYL 87
+S ++++ KK ++ L +Y + +Y+ T + I E+ + I +
Sbjct: 129 YSISDSSSKKKFETSQSNLKDYADTFFRYLRYTGLFSIRGNGKLIIINPEKKEEIDEI 186
>gnl|CDD|146353 pfam03673, UPF0128, Uncharacterized protein family (UPF0128).
The members of this family are about 240 amino acids in
length. The proteins are as yet uncharacterized.
Length = 221
Score = 25.9 bits (57), Expect = 2.9
Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 2/72 (2%)
Query: 18 GPNLHGLIGRKTGQAPGFSYTEANIKKGITWNKDTLFEYLENPKKYIPGTKMIFAGIKKP 77
G +L +G+K G+ F + G ++KD +E K +P K +FA I+
Sbjct: 29 GFDLI--LGKKDGERAYFVSELGGREVGDKFSKDGKEYEIEEILKELPKNKKLFAHIEME 86
Query: 78 QERGDLIAYLEQ 89
+ + L+ +L +
Sbjct: 87 EGQAYLVFWLRE 98
>gnl|CDD|150363 pfam09675, Chlamy_scaf, Chlamydia-phage Chp2 scaffold
(Chlamy_scaf). Members of this entry are encoded by
genes in chlamydia-phage such as Chp2. These viruses
have around eight genes and obligately infect
intracellular bacterial pathogens of the genus
Chlamydia. This protein is annotated as VP3 or
structural protein (as if a protein of mature viral
particles), however, it is displaced from procapsids as
DNA is packaged, and therefore is more correctly
described as a scaffolding protein.
Length = 107
Score = 25.2 bits (55), Expect = 4.1
Identities = 8/47 (17%), Positives = 19/47 (40%), Gaps = 8/47 (17%)
Query: 40 ANIKKGITWNKDTLFEYLENPKKY--------IPGTKMIFAGIKKPQ 78
A I++ + + + E+L +P+ Y + I K+ +
Sbjct: 52 AKIRERFGNDPEEMLEFLNDPENYDEAVSLGLLKTEMRIEVQRKRLK 98
>gnl|CDD|180330 PRK05965, PRK05965, hypothetical protein; Provisional.
Length = 459
Score = 25.8 bits (57), Expect = 4.2
Identities = 12/44 (27%), Positives = 17/44 (38%), Gaps = 5/44 (11%)
Query: 22 HGLIGRKTGQ-----APGFSYTEANIKKGITWNKDTLFEYLENP 60
+GL+ R G AP TE + TL + L +P
Sbjct: 409 NGLVFRAFGDGVLGFAPALCCTEGEFDLIFERTRKTLDDVLADP 452
>gnl|CDD|236211 PRK08268, PRK08268, 3-hydroxy-acyl-CoA dehydrogenase; Validated.
Length = 507
Score = 25.6 bits (57), Expect = 4.5
Identities = 9/19 (47%), Positives = 12/19 (63%), Gaps = 3/19 (15%)
Query: 23 GLIGRKTGQAPGF-SYTEA 40
G +GRK+GQ GF Y +
Sbjct: 274 GRLGRKSGQ--GFYRYADG 290
>gnl|CDD|239428 cd03312, CIMS_N_terminal_like, CIMS - Cobalamine-independent
methonine synthase, or MetE, N-terminal domain_like.
Many members have been characterized as
5-methyltetrahydropteroyltriglutamate-homocysteine
methyltransferases, EC:2.1.1.14, mostly from bacteria
and plants. This enzyme catalyses the last step in the
production of methionine by transferring a methyl group
from 5-methyltetrahydrofolate to L-homocysteine without
using an intermediate methyl carrier. The active enzyme
has a dual (beta-alpha)8-barrel structure, and this
model covers the N-terminal barrel, and a few
single-barrel sequences most similar to the N-terminal
barrel. It is assumed that the homologous N-terminal
barrel has evolved from the C-terminus via gene
duplication and has subsequently lost binding sites, and
it seems as if the two barrels forming the active enzyme
may sometimes reside on different polypeptides. The
C-terminal domain incorporates the Zinc ion, which binds
and activates homocysteine. Side chains from both
barrels contribute to the binding of the folate
substrate.
Length = 360
Score = 25.6 bits (57), Expect = 4.5
Identities = 6/18 (33%), Positives = 9/18 (50%)
Query: 57 LENPKKYIPGTKMIFAGI 74
LE K K++ AG+
Sbjct: 269 LEAVLKAGFADKVLSAGV 286
>gnl|CDD|234392 TIGR03908, QH_alpha, quinohemoprotein amine dehydrogenase, alpha
subunit. Quinohemoprotein amine dehydrogenase is a
three subunit enzyme with both a heme group and a
cysteine tryptophylquinone group derived by
post-translational modification of the gamma subunit.
This model describes the beta subunit. This enzyme
catalyzes oxidative deamination of primary aliphatic
and aromatic amines (PMID:10346915) [Energy metabolism,
Amino acids and amines].
Length = 510
Score = 25.2 bits (55), Expect = 7.3
Identities = 7/13 (53%), Positives = 8/13 (61%)
Query: 2 KCAQCHTIEAGGA 14
KC CHT +A G
Sbjct: 15 KCGACHTADAKGK 27
>gnl|CDD|163518 TIGR03806, chp_HNE_0200, conserved hypothetical protein, HNE_0200
family. The model TIGR03805 describes an
uncharacterized protein family that contains repeats
associated with the formation of a right-handed helical
stack of parallel beta strands, homologous to those
found in a number of carbohydrate-binding proteins and
sugar hydrolases. This model describes another
uncharacterized protein family, found in the same
species as TIGR03805 member proteins, usually as the
adjacent gene or in a fusion protein. An example is
HNE_0200 from Hyphomonas neptunium ATCC 15444. Sometimes
two members of this family are with a single member of
TIGR03805. The function is unknown [Hypothetical
proteins, Conserved].
Length = 317
Score = 24.7 bits (54), Expect = 8.2
Identities = 8/23 (34%), Positives = 11/23 (47%), Gaps = 1/23 (4%)
Query: 2 KCAQCHTIEAGGAHKVGPNLHGL 24
+C QCH + A +GP L
Sbjct: 145 QCKQCHQL-AADIVPLGPKARQL 166
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 0.136 0.416
Gapped
Lambda K H
0.267 0.0698 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,686,121
Number of extensions: 376023
Number of successful extensions: 362
Number of sequences better than 10.0: 1
Number of HSP's gapped: 359
Number of HSP's successfully gapped: 23
Length of query: 92
Length of database: 10,937,602
Length adjustment: 59
Effective length of query: 33
Effective length of database: 8,320,716
Effective search space: 274583628
Effective search space used: 274583628
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 (24.3 bits)