RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7278
(106 letters)
>gnl|CDD|238466 cd00926, Cyt_c_Oxidase_VIb, Cytochrome c oxidase subunit VIb.
Cytochrome c oxidase (CcO), the terminal oxidase in the
respiratory chains of eukaryotes and most bacteria, is a
multi-chain transmembrane protein located in the inner
membrane of mitochondria and the cell membrane of
prokaryotes. It catalyzes the reduction of O2 and
simultaneously pumps protons across the membrane. The
number of subunits varies from three to five in bacteria
and up to 13 in mammalian mitochondria. Subunits I, II,
and III of mammalian CcO are encoded within the
mitochondrial genome and the remaining 10 subunits are
encoded within the nuclear genome. Found only in
eukaryotes, subunit VIb is one of three mammalian
subunits that lacks a transmembrane region. It is
located on the cytosolic side of the membrane and helps
form the dimer interface with the corresponding subunit
on the other monomer complex.
Length = 75
Score = 71.2 bits (175), Expect = 7e-18
Identities = 28/65 (43%), Positives = 38/65 (58%)
Query: 36 DPRFQQVNITNWCWTMFVDHKRCSNLLGEGRADCAIFKKCYESICPNAWVEQWEDQIENN 95
DPRF N T CW +VD+ RC GE + C F++ YES+CP W+E+W++Q E
Sbjct: 11 DPRFPNQNQTKHCWQRYVDYHRCIKAKGEDASPCKKFRRVYESLCPQEWLEKWDEQREEG 70
Query: 96 IFPRD 100
FP
Sbjct: 71 TFPGK 75
>gnl|CDD|216964 pfam02297, COX6B, Cytochrome oxidase c subunit VIb. Cytochrome c
oxidase, a 13 sub-unit complex, EC:1.9.3.1 is the
terminal oxidase in the mitochondrial electron
transport chain. This family is composed of the
potentially heme-binding subunit IVb of the oxidase.
Length = 66
Score = 55.4 bits (134), Expect = 8e-12
Identities = 23/55 (41%), Positives = 31/55 (56%)
Query: 37 PRFQQVNITNWCWTMFVDHKRCSNLLGEGRADCAIFKKCYESICPNAWVEQWEDQ 91
PRF N CW D +C + GE + C FKK YES+CP +WVE +++Q
Sbjct: 1 PRFPNQNQRKHCWQARDDFFKCLDKNGEDNSPCKKFKKNYESLCPASWVEYFDEQ 55
>gnl|CDD|182207 PRK10045, PRK10045, acyl carrier protein phosphodiesterase;
Provisional.
Length = 193
Score = 28.3 bits (63), Expect = 0.68
Identities = 15/35 (42%), Positives = 21/35 (60%), Gaps = 9/35 (25%)
Query: 23 PLEE-----HKQLSTCLPD--PRFQQVNITNWCWT 50
PL+E +Q+ T LPD PRF VN+ N+ W+
Sbjct: 97 PLQEFVCYAREQVMTILPDSPPRF--VNLNNYLWS 129
>gnl|CDD|137339 PRK09499, sifB, secreted effector protein SifB; Provisional.
Length = 316
Score = 27.7 bits (61), Expect = 1.1
Identities = 16/77 (20%), Positives = 32/77 (41%), Gaps = 8/77 (10%)
Query: 26 EHKQLSTCLPDPRFQQVNITNWCWTMFVDHKRCSNLLGEGRADCAIFKKCYESICPNAWV 85
E+ L +P + Q ++T ++ ++ N+L E + +C N
Sbjct: 234 ENTNLKNAAFEPNYAQSSVTQIVYSCLFKNEILMNMLEE--------SSSHGLLCLNELT 285
Query: 86 EQWEDQIENNIFPRDLT 102
E Q+ N++F DL+
Sbjct: 286 EYVALQVHNSLFSEDLS 302
>gnl|CDD|236548 PRK09525, lacZ, beta-D-galactosidase; Reviewed.
Length = 1027
Score = 26.8 bits (60), Expect = 2.5
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 77 ESICPNAWVEQWE 89
I PNAWVE+W+
Sbjct: 803 TRIDPNAWVERWK 815
>gnl|CDD|222234 pfam13575, DUF4135, Domain of unknown function (DUF4135). This
presumed domain is functionally uncharacterized. This
domain family is found in bacteria and archaea, and is
approximately 380 amino acids in length. The family is
found in association with pfam05147. This domain may be
involved in synthesis of a lantibiotic compound.
Length = 369
Score = 26.1 bits (58), Expect = 4.3
Identities = 8/27 (29%), Positives = 16/27 (59%), Gaps = 2/27 (7%)
Query: 34 LPDPRFQQVNITNWCWTMFVDHKRCSN 60
LP R ++ ++ W F++HK C++
Sbjct: 103 LPTLRV--LDRGDYGWEEFIEHKPCAS 127
>gnl|CDD|238629 cd01304, FMDH_A, Formylmethanofuran dehydrogenase (FMDH) subunit
A; Methanogenic bacteria and archea derive the energy
for autotrophic growth from methanogenesis, the
reduction of CO2 with molecular hydrogen as the
electron donor. FMDH catalyzes the first step in
methanogenesis, the formyl-methanofuran synthesis. In
this step, CO2 is bound to methanofuran and
subsequently reduced to the formyl state with electrons
derived from hydrogen.
Length = 541
Score = 25.8 bits (57), Expect = 5.6
Identities = 8/23 (34%), Positives = 12/23 (52%), Gaps = 1/23 (4%)
Query: 4 TNGVELQPGE-FIRDGMICKPLE 25
NG+ + + FIRDG I +
Sbjct: 10 LNGINGEKMDIFIRDGKIVESSS 32
>gnl|CDD|218978 pfam06294, DUF1042, Domain of Unknown Function (DUF1042). Spef is
a region of sperm flagellar proteins. It probably exerts
a role in spermatogenesis in that the protein is
expressed predominantly in adult tissue. It is present
in the tails of developing and epididymal sperm internal
to the fibrous sheath and around the dense outer fibres
of the sperm flagellum. The amino-terminal domain
(residues 1-110) shows a possible calponin homology (CH)
domain; however Spef does not bind actin directly under
in vitro conditions, so the function of the
amino-terminal calponin-like domain is unclear.
Transcription aberrations leading to a truncated protein
result in immotile sperm.
Length = 154
Score = 24.7 bits (54), Expect = 9.5
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 85 VEQWEDQIENNIFPRDLTR 103
+ QW Q +I PR+L R
Sbjct: 1 LNQWLQQESRSISPRNLRR 19
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
0.323 0.138 0.480
Gapped
Lambda K H
0.267 0.0755 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,257,034
Number of extensions: 403481
Number of successful extensions: 259
Number of sequences better than 10.0: 1
Number of HSP's gapped: 259
Number of HSP's successfully gapped: 13
Length of query: 106
Length of database: 10,937,602
Length adjustment: 71
Effective length of query: 35
Effective length of database: 7,788,468
Effective search space: 272596380
Effective search space used: 272596380
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.1 bits)